-
Notifications
You must be signed in to change notification settings - Fork 3
/
Copy pathNEWS
4223 lines (2629 loc) · 142 KB
/
NEWS
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
Package: aroma.affymetrix
=========================
Version: (development version)
* ...
Version: 3.2.2 [2024-02-18]
DOCUMENTATION:
* Fix minor Rd help-page issues.
Version: 3.2.1 [2022-07-18]
PERFORMANCE:
* MEMORY: Some parameter estimates where pre-allocated as logical (NA)
values, instead of as numeric (NA_real_) values, which would result in
an unnecessary coercion from logical to numeric.
Version: 3.2.0 [2019-06-22]
NEW FEATURES:
* Windows Shortcut links (*.lnk) to CEL files are now also recognized
as CEL files.
BUG FIXES:
* findByChipType() for AffymetrixCdfFile and AffymetrixPdfFile would
only recognize Windows Shortcut Links with a filename extension
in lower case (*.lnk) but not in upper case (*.LNK).
* TESTS: Package test on CEL files would produce an error on MS Windows
if only Windows Shortcut links were supported but not symbolic links.
Version: 3.1.1 [2018-04-16]
SIGNIFICANT CHANGES:
* Package requires R (>= 3.2.0) and BioC (>= 3.1) both released
in April 2015.
BUG FIXES:
* Removed invalid 'break' statement in getAlleleProbePairs() for
AffymetrixCdfFile.
CODE REFACTORING:
* Using indexByRow(dim(x)) internally since indexByRow(x) will soon be
deprecated in matrixStats.
DEPRECATED AND DEFUNCT:
* Passing argument 'ram' to any of the doNnn() methods is now defunct and
gives an informative error message. It has been given a warning since
v2.8.4 (May 2013). Use setOption(aromaSettings, 'memory/ram', ram).
* Monocell CDF files named with a very very old "-monocell.cdf" suffix are
now ignored. There has been an informative error that these are defunct
since v 2.6.3 (October 2012).
Version: 3.1.0 [2017-03-23]
NEW FEATURES:
* Now file and object sizes are reported using IEC binary prefixes,
i.e. bytes, KiB, MiB, GiB, TiB, ..., YiB.
* Now doNnn() methods can be called directly from the command line, e.g.
Rscript -e aroma.affymetrix::doCRMAv2 --dataSet=HapMap270
--chipType=GenomeWideSNP_6
* Objects no longer report on memory (RAM) usage.
REFACTORIZATION:
* Used partial element name 'coef' instead of 'coefficients' for lm() fit.
BUG FIXES:
* Package used %<=% internally with was deprecated in future (>= 1.4.0).
* ROBUSTNESS: Some regular expression patterns used for locating files
would match any symbol when it intended to match only a period.
* The International HapMap Project (http://www.hapmap.org/) is being retired
and HTTP server http://hapmap.ncbi.nlm.nih.gov/downloads/raw_data/ is
decomissioned. System test scripts updated to download HapMap CEL files
from the FTP server ftp://ftp.ncbi.nlm.nih.gov/hapmap/raw_data/ instead.
DEPRECATED AND DEFUNCT:
* Methods bgAdjustRma(), bgAdjustOptical() and bgAdjustGcrma() for
AffymetrixCelFile as well as bgAdjustGcrma() for AffymetrixCelSet
are now defunct.
Version: 3.0.0 [2016-01-09]
SIGNIFICANT CHANGES:
* Package requires R (>= 3.1.2) and BioC (>= 3.0) both released
in October 2014.
NEW FEATURES:
* REPRODUCIBILITY: GcRmaBackgroundCorrection(), LimmaBackgroundCorrection(),
and RmaBackgroundCorrection() gained argument 'seed'.
* REPRODUCIBILITY: Several of the methods now generate *.md5 checksum
files for the data files they output.
* Now also convertToUnique() acknowledge asterisk tags.
PERFORMANCE:
* SPEED: Adding support for parallel/distributed processing via futures
to some of the methods for which it is possible to process each
sample independently, e.g. background and crosstalk correction methods.
REFACTORIZATION:
* ROBUSTNESS: Using do.call(fcn) internally instead of do.call("fcn").
* CLEANUP: Warnings on "is.na() applied to non-(list or vector) of
type 'NULL'" are no longer generated.
SOFTWARE QUALITY:
* ROBUSTNESS: MatNormalization did not create CEL files atomically.
BUG FIXES:
* LimmaBackgroundCorrection(..., addJitter=TRUE) gave an error.
DEPRECATED AND DEFUNCT:
* CLEANUP: Formally defunct'ed bgAdjustRma(), bgAdjustGcrma(),
bgAdjustOptical() for AffymetrixCelFile/AffymetrixCelSet since they
have effectively been defunct'ed in the public API for years. These
are now all incorporated in corresponding BackgroundCorrection classes.
Version: 2.14.0-9000 [2015-12-23]
* ROBUSTNESS: Using getPathname() instead of accessing private field.
BUG FIXES:
* convertToUnique() for AffymetrixCelSet would give an error if there was
an error while checking if results already exist.
Version: 2.14.0 [2015-10-24]
* AvgPlm, used by for instance doCRMAv2(), would give harmless warning
"Argument 'centers' for matrixStats::rowMads() has been renamed to
'center'. Please update code accordingly."
* ROBUSTNESS: fitCnProbes() for UnitModel could in rare cases give an
error on one of the internal sanity checks.
SOFTWARE QUALITY:
* ROBUSTNESS: Explicitly importing core R functions.
BUG FIXES:
* extractAlleleSet() for SnpChipEffectSet now needs to load namspace
'oligoClasses' explicitly.
* writeCdf() for AffyGenePDInfo gave "Error in affxparser::writeCdf(...) :
unused argument (pathname = ..." due to a bug/typo introduced in 2.13.2.
Thanks to Guillaume Devailly for reporting on this.
DEPRECATED AND DEFUNCT:
* Removed methods marked as defunct in v2.11.3 (Feb 2014).
Version: 2.13.2 [2015-05-26]
SIGNIFICANT CHANGES:
* Package now requires R (>= 3.1.1) released July 2014. This allows
us to use BioC (>= 3.0) (October 2014).
SOFTWARE QUALITY:
* ROBUSTNESS: Many functions now assert that they don't return file
data sets with duplicated entries.
* ROBUSTNESS: Package now declares all S3 methods.
Version: 2.13.1 [2015-01-23]
* Now a pre-existing monocell CDF can be recreated and overwritten
using getMonocellCdf(cdf, force=TRUE).
BUG FIXES:
* getMonocellCdf() for AffymetrixCdfFile would throw "Error in (...) :
3 arguments passed to '(' which requires 1". This was due to a typo
(erroneous newline) introduced in 2.13.0. Add package tests for this.
Thanks to Qingzhou Zhang for reporting on this.
Version: 2.13.0 [2015-01-17]
* Bumped version for CRAN submission.
* Updated package dependencies.
SOFTWARE QUALITY:
* Package passes all redundancy tests.
Version: 2.12.10 [2015-01-06]
* CLEANUP: Major cleanup of namespace imports from suggested packages
such as affxparser and aroma.light.
Version: 2.12.9 [2014-11-17]
* Updated redundancy tests under testScripts/ to find rowMedians() of
the matrixStats package. The matrixStats package used to be attached
whenever aroma.light (< 2.1.1) was attached, but no longer.
Version: 2.12.8 [2014-09-04]
BUG FIXES:
* ROBUSTNESS/BUG FIX: createFrom(..., mode="copy") for AffymetrixCelFile
would give an error on "No permission to modify existing file: ..."
iff the source file had read-only permission. This bug was introduced
by changes to base::file.copy() in R (>= 2.13.0) [April 2011].
Thanks to Taylor Raborn at Indiana University for reporting on this.
Version: 2.12.7 [2014-08-27]
BUG FIXES:
* Added forgotten NAMESPACE imports.
Version: 2.12.6 [2014-06-29]
BUG FIXES:
* getAromaCellSequenceFile() for AffymetrixCdfFile used undefined variable
'nbrOfCells'.
Version: 2.12.5 [2014-06-24]
SOFTWARE QUALITY:
* Added package system tests utilizing example data of Bioconductor
package AffymetrixDataTestFiles, iff installed.
Version: 2.12.4 [2014-06-09]
SIGNIFICANT CHANGES:
* Package now requires R (>= 3.0.0) and BioC (>= 2.13), which were
released April 2013 and are in fact old and it's recommended to
use a more recent version of R.
* Added 'SuggestsNote' field to DESCRIPTION with list of packages
that are recommended for the most common use cases.
* Bumped package dependencies.
Version: 2.12.3 [2014-05-02]
* CLEANUP: Now using ds[[idx]] instead of getFile(ds, idx) where possible.
Version: 2.12.2 [2014-04-28]
* Added justRMA() for AffymetrixCelSet, which with good precision
reproduces the results of the default setting of justRMA() in the
affy package. It does so by still running with a constant memory
profile. This means that a much larger number of samples can be
processed using this implementation.
* doCRMAv2(..., drop=FALSE) and hence doASCRMAv2(..., drop=FALSE), did
not *return* the base-position normalization step, although it was
done and its outcome was part of all downstream steps.
* extractExpressionSet() for ChipEffectSet gained argument 'orderUnitsBy'
and returns standard errors as well.
Version: 2.12.1 [2014-04-26]
* SPEEDUP: Minor speedup by replacing repetive <ns>::<fcn>() calls
with repetive <fcn>() calls; the '::' operator is fairly expensive.
You should expect a small speed improvement when using MatSmoothing(),
RmaPlm(..., flavor="oligo") and when calculating weights using
ExonRmaPlm and QualityAssessmentModel, to name a few examples.
Version: 2.12.0 [2014-03-07]
* Bumped version for CRAN submission.
* Updated package dependencies.
SOFTWARE QUALITY:
* Package passes all redundancy tests.
Version: 2.11.3 [2014-02-28]
* Now methods that supports searching sibling root directories do so by
default. Previously this had to be explicitly enabled via an option.
DEPRECATED AND DEFUNCT:
* CLEANUP: Removed defunct methods. Made previously deprecated defunct.
Version: 2.11.2 [2014-01-04]
DEPRECATED AND DEFUNCT:
* CLEANUP: Dropped defunct methods '[' and '[[' for AffymetrixCelSet
and CnagCfhSet (which have been defunct since 2013-04-29).
Version: 2.11.1 [2013-10-17]
* DOCUMENTATION: Minor tweaks to the help for the doNNN() methods.
Version: 2.11.0 [2013-10-17]
SIGNIFICANT CHANGES:
* Package now requires R (>= 2.15.0) [and Bioc (>= 2.10.0)].
* Updated package dependencies.
Version: 2.10.3 [2013-10-07]
* CLEANUP: No longer need to attach R.utils for backward compatibility.
* CLEANUP: Package no longer apply downloaded package patches.
* CLEANUP: Now explicitly importing only what is needed in NAMESPACE.
* CLEANUP: No longer uses ':::' for accessing 'oligo' functions.
* Updated package dependencies.
DEPRECATED AND DEFUNCT:
* CLEANUP: Deprecated patch() for AromaAffymetrix.
Version: 2.10.2 [2013-09-28]
* Now the 'aroma.affymetrix' Package object is also available when the
package is only loaded (but not attached).
* Updated package dependencies.
Version: 2.10.1 [2013-08-21]
* Now explicitly importing R.filesets and aroma.core in NAMESPACE.
Version: 2.10.0 [2013-08-04]
* CLEANUP: The formal package dependency on Bioconductor packages
'aroma.light' and 'affxparser' has been relaxed so the package
can be installed without them.
* CLEANUP: Package now only imports matrixStats, R.oo, R.filesets
and aroma.apd.
* Bumped version for CRAN submission.
* Updated package dependencies.
SOFTWARE QUALITY:
* Package passes all redundancy tests.
DEPRECATED AND DEFUNCT:
* CLEANUP: Removed since-long defunct methods. Made deprecated
methods defunct.
Version: 2.9.7 [2013-07-28]
* ROBUSTNESS: byPath() for DChipDcpSet was not declared static.
BUG FIXES:
* In certain cases, calls to static method byPath() would be affected by the
NextMethod() '...' bug reported in R-devel thread "Do *not* pass '...' to
NextMethod() - it'll do it for you; missing documentation, a bug or just
me?" on 2012-10-16.
Version: 2.9.6 [2013-07-03]
* Added argument 'flavor' or doRMA() making it easier to replicate the
results of other packages, e.g. doRMA(..., flavor="oligo").
Version: 2.9.5 [2013-06-02]
* ROBUSTNESS: Now more methods are creating/writing signals atomically.
BUG FIXES:
* Since v2.9.0, doFIRMA() would give "Exception: Unknown arguments:
.onUnknownArgs" in the alternative splicing step.
* calculateConfidenceScores() for CrlmmModel used defunct method
isHeterozygote() instead of isHeterozygous().
* Certain methods could throw 'Error in UseMethod("getChecksum"): no
applicable method for 'getChecksum' applied to an object of class "list"'
if (and only if) R.cache package was not attached. The same bug was
fixed on aroma.core v2.9.2 recently.
Version: 2.9.4 [2013-05-30]
* Now it's possible to call aroma.affymetrix::doRMA() without first
loading package. Same for all other doNnn() methods, e.g. doCRMAv2(),
doFIRMA() and doGCRMA().
Version: 2.9.3 [2013-05-25]
* SPEEDUP: Replaced all rm() calls with NULL assignments.
Version: 2.9.2 [2013-05-22]
* CLEANUP: Now using getChecksum() instead of (internal)
R.filesets::digest2() with identical results.
* CLEANUP: Now getIdentifier() for CnagCfhFile utilizes
getChecksum() for the GenericDataFile class.
Version: 2.9.1 [2013-05-20]
SOFTWARE QUALITY:
* CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
Version: 2.9.0 [2013-05-02]
* Submitted to CRAN.
SOFTWARE QUALITY:
* The package passes all redundancy tests.
Version: 2.8.4 [2013-05-02]
* DOCUMENTATION: Now doRMA(), doGCRMA(), doFIRMA(),
doCRMAv1()/doASCRMAv1() and doCRMAv2()/doASCRMAv2() are
fully documented and listed in the help index.
* Added argument 'annotationPkg' to extractExpressionSet() for
ChipEffectSet, which (indirectly) sets the 'annotation' slot
of the returned ExpressionSet.
* Added extractFeatureSet() for AffymetrixCelSet.
* SPEEDUP: Added ^Cyto.*Array$ to list of SNP chips that isSnpChip()
for AffymetrixCdfFile knows of without having to scan the CDF.
* SPEEDUP: Just as doCRMAv2()/doASCRMAv2(), now also doRMA() and
doGCRMA() return much quicker if already processed.
DEPRECATED AND DEFUNCT:
* CLEANUP: Removed argument 'ram' from doNnn() methods in favor
setOption(aromaSettings, 'memory/ram', ram).
* CLEANUP: Made several deprecated methods defunct.
Version: 2.8.3 [2013-04-01]
* Force creation of a generic process(), because depending on the
version of R.rsp at the time of the build, process() may be missing
or not.
* Bumped up package dependencies.
Version: 2.8.2 [2013-03-22]
* Obscufated the error message on ASCII CDFs on how to change settings
to allow the processing of such, because it shouldn't be easy to
do that.
Version: 2.8.1 [2013-03-05]
* DOCUMENTATION: Updated the help usage section for all static methods.
* Bumped up package dependencies.
Version: 2.8.0 [2012-12-21]
* No updates.
* Bumped version for CRAN submission.
SOFTWARE QUALITY:
* Package passes all redundancy tests.
Version: 2.7.9 [2012-12-21]
* Bumped package dependencies.
* Utilizing new startupMessage() of R.oo.
* ROBUSTNESS: Now all internal pathnames are shorter than 100
characters, which is the upper limit that 'tar' supports.
DEPRECATED AND DEFUNCT:
* Now using argument 'colClasses' (was 'colClassPatterns')
for all readDataFrame():s and elsewhere.
Version: 2.7.8 [2012-12-18]
* ROBUSTNESS: Added argument 'unitsBy' (and 'namesBy') to writeCdf()
for AffyGenePDInfo, where 'unitsBy' defaults to "transcript". It
now also drops any duplicated probe entries. Furthermore, calling
writeCdf() for other classes of DBPDInfo objects will now give a
more informative error message that those classes are yet not
supported. Thanks Guido Hooiveld (Wageningen University, Netherlands)
for suggestions and tests.
* Now validate() for AffymetrixCdfFile accepts empty unit names as
long as the unit is not empty.
BUG FIXES:
* writeCdf(..., useTranscriptCluster=FALSE) for AffyGenePDInfo could
generate empty unit names files for units with 'fsetid' <= 9999.
Version: 2.7.7 [2012-12-10]
BUG FIXES:
* getTimestamp() for AffymetrixCelFile would throw an error if the CEL file
header did not have a timestamp. Thanks Guido Hooiveld (Wageningen
University, Netherlands) for reporting this.
Version: 2.7.6 [2012-12-06]
* ROBUSTNESS: Utilizing new getOneFile() internally.
Version: 2.7.5 [2012-12-01]
BUG FIXES:
* BUG FIX/ROBUSTNESS: convertToUnique() for AffymetrixCelSet would
return all CEL files found in the output directory, not just the ones
corresponding to the input set, and possibly in a different order.
Version: 2.7.4 [2012-11-29]
* DOCUMENTATION: Added help pages to more methods.
* ROBUSTNESS: updateUnits() for ResidualSet did not update the files in
lexicographic order as previously claimed.
Version: 2.7.3 [2012-11-28]
* ROBUSTNESS: Added system test scripts for building UGP and UFL
file from Affymetrix CSF and NetAffx CSV files for GenomeWideSNP_6.
BUG FIXES:
* Static allocateFromCdf() for AromaUfcFile and AromaUflFile would throw
errors on "Cannot retrieve writable file/directory because it is NA.".
This turns out to be related to the trap reported in R-devel thread
'Do *not* pass '...' to NextMethod() - it'll do it for you; missing
documentation, a bug or just me?' on Oct 16, 2012. Thanks Ioana
Cutcutache (Duke-NUS in Singapore) for reporting on this.
Version: 2.7.2 [2012-11-28]
* ROBUSTNESS: Added the FileCacheKeyInterface to all classes directly
extending GenericDataFile and TabularTextFile.
* MEMORY: readUnits() for ChipEffectFile, FirmaFile, ParameterCelFile,
ResidualFile, and WeightsFile no longer cache results in memory
by default.
Version: 2.7.1 [2012-11-26]
* Lowered the package dependencies to aroma.light (>= 1.22.0)
and affxparser (>= 1.26.4) so that this package can be easily
installed on R (>= 2.14.0).
Version: 2.7.0 [2012-11-24]
* Bumped version for CRAN submission.
* Bumped up package dependencies.
SOFTWARE QUALITY:
* Package passes all redundancy tests.
Version: 2.6.16 [2012-11-21]
* Updated verbose output of parameters.
Version: 2.6.14 [2012-11-21]
* DOCUMENTATION: Hiding more internal methods from the help indices.
* CLEANUP: Now utilizing the new ParametersInterface.
* CLEANUP: Replaced all getParameterSet() with getParameters().
* CLEANUP: bgAdjustGcrma() for AffymetrixCelSet no longer reads
and write probe affinity files in the deprecated APD format.
* CLEANUP: Removed obsolete code from internal bgAdjustOptical() that
was never reached and that loaded affinities via obsolete APD files.
DEPRECATED AND DEFUNCT:
* CLEANUP: bgAdjustOptical() and bgAdjustRma() for AffymetrixCelSet
are now defunct. Instead, see OpticalBackgroundCorrection and
RmaBackgroundCorrection.
* CLEANUP: Deprecated "[" and "[[" for AffymetrixCelFile,
AffymetrixCelSet, CnagCfhFile, and CnagCfhSet.
Version: 2.6.13 [2012-11-18]
* Now package explicitly imports R.cache, because aroma.core is no
longer loading it.
Version: 2.6.12 [2012-11-14]
* CLEANUP: getWeights() for QualityAssessmentModel no longer sets the
alias of the returned data set, because the use of aliases is deprecated.
* CLEANUP: writeImage() for AffymetrixCelFile no longer supports
sample name aliases.
Version: 2.6.11 [2012-11-13]
* CLEANUP: Properly declared all cached fields, making it possible
to remove nearly all clearCache() implementations because the one
for Object takes does the job.
Version: 2.6.10 [2012-11-12]
* CLEANUP: Now seq_along(x) instead of seq(along=x) everywhere.
Similarly, seq(ds) where 'ds' is GenericDataFileSet is now
replaced by seq_along(ds). Likewise, seq_len(x) replaces
seq(length=x), and length(ds) replaces nbrOfFiles(ds).
Version: 2.6.9 [2012-11-08]
* Renamed getColumnNames() to getDefaultColumnNames() for all
classes inheriting from GenericTabularFile, because of the
new ColumnNamesInterface interface.
Version: 2.6.8 [2012-11-05]
* CLEANUP: Replaced all whichVector() with which(), because the
latter is now the fastest again.
Version: 2.6.7 [2012-10-29]
* CLEANUP: Now using Arguments$get(Read|Writ)ablePath() instead of
filePath(..., expandLinks="any").
Version: 2.6.6 [2012-10-21]
* ROBUSTNESS: Now using Arguments$getWritablePath() everywhere instead
of mkdirs(), because the former will do a better job in creating
and asserting directories on slow shared file systems, and when it
fails it gives a more informative error message.
Version: 2.6.5 [2012-10-18]
* ROBUSTNESS: Now createMonocellCdf() for AffymetrixCdfFile validates
the CDF (via new validate()). This will give more informative
error message in case the CDF is invalid, e.g. containing "empty"
units.
* ROBUSTNESS: Added validate() for AffymetrixCdfFile, which validate
a CDF for the most "common" errors, to help troubleshooting. Note
that the validation is not complete, i.e. rare/unknown errors are
not caught.
* Now as.character() for all AromaChipTypeAnnotationFile classes,
and hence print(), reports the file size both as abbreviated as
well as in exact number of bytes, e.g. "24.66 MB (25853850 bytes)"
(used to only be "24.66 MB").
Version: 2.6.4 [2012-10-16]
BUG FIXES:
* ROBUSTNESS/BUG FIX: No longer passing '...' to NextMethod(), cf.
R-devel thread 'Do *not* pass '...' to NextMethod() - it'll do it
for you; missing documentation, a bug or just me?' on Oct 16, 2012.
Version: 2.6.3 [2012-10-14]
* CLEANUP: Moved AromaUnitGcContentFile to aroma.core.
DEPRECATED AND DEFUNCT:
* CLEANUP: Removed several defunct/obsolete methods and turned
deprecated methods into defunct/obsolete ones.
* CLEANUP: findByChipType() for AffymetrixCdfFile no longer support
monocell CDF file named <chipType>-monocell.CDF, and gives an
informative error if that is still the case. Since December 2007,
the filename should instead be <chipType>,monocell.CDF.
* CLEANUP: createParamCdf() for ChipEffectFile and FirmaFile no longer
support '<chipType>-monocell' filenames. If detected, an informative
error is thrown.
Version: 2.6.2 [2012-09-15]
BUG FIXES:
* doCRMAv2() failed to quickly located already available results if the
chip type of the CDF had tags, e.g. 'GenomeWideSNP_6,Full'.
Version: 2.6.1 [2012-09-14]
* MEMORY: Now getUnitIntensities() and readUnits() for AffymetrixCelSet
no longer cache the results in memory if argument 'units' is NULL.
* CLEANUP: Restructured part of the test scripts tree. Added a new
batch launcher.
BUG FIXES:
* BUG FIX/ROBUSTNESS: Although getUnitIntensities() for AffymetrixCelSet
would retrieve the CDF tree structure and pass it to affxparser's
readCelIntensities(), it was done in such a way that the latter would
still need to find and read the CDF. This meant that it would not
necessarily retrieve the same CDF as the AffymetrixCelSet used.
* The utility function for downloading individual CEL files from GEO would
give an error that it could not gunzip the downloaded file, iff the
filename extension was lower case, e.g. *.cel.gz instead of *.CEL.gz.
Version: 2.6.0 [2012-09-05]
* Submitted to CRAN.
SOFTWARE QUALITY:
* The package passes all redundancy tests.
Version: 2.5.11 [2012-09-05]
* ROBUSTNESS: Now doCRMAv1() adds also tag "v1" to the allele-specific
calibration step. The reason for this is to differentiate it from
the output of doCRMAv2(). NOTE: This update means that any old CRMAv1
analyzes will not be detected by doCRMAv1(); to have doCRMAv1() detect
those add tag "v1" in that calibration step, e.g. "ACC,-XY,v1".
* ROBUSTNESS: Now the CrlmmModel constructor asserts that the chip
effects were estimated without merging the strands (mergeStrands=FALSE).
If not, an informative exception is thrown.
Version: 2.5.10 [2012-09-04]
SOFTWARE QUALITY:
* CLEANUP/ROBUSTNESS: Updated test scripts by rewriting some tests
to be more clear/consistent on what they are testing and by
cleaning out tests that duplicates each other etc.
* Added system test scripts that automatically download the needed
test data sets and install some extra packages needed for some
of the tests.
BUG FIXES:
* BUG FIX/ROBUSTNESS: extractAlleleSet(), extractSnpCnvQSet() and
extractSnpQSet() for SnpChipEffectSet would throw an exception
iff the 'Biobase' package was not loaded.
Version: 2.5.9 [2012-08-31]
SOFTWARE QUALITY:
* Added system test scripts that automatically download the needed
annotation data files iff missing. This simplifies running the
package's system tests on a new system.
Version: 2.5.8 [2012-08-30]
* CLEANUP: Package no longer masks boxplot.stats(), getPackageName()
and write() from other packages.
* CLEANUP: Dropped system tests that did not test what other
tests already test.
DEPRECATED AND DEFUNCT:
* CLEANUP: Dropped readCdfDataFrame(), which is identical to
the one in affxparser, which has remained the same since
affxparser v1.21.1 (Oct 2010).
Version: 2.5.7 [2012-08-28]
* SPEED UP: Now doCRMAv2() returns even faster if already processed.
SOFTWARE QUALITY:
* Added systems test for running doASCRMAv2() in parallel using parLapply().
Version: 2.5.6 [2012-08-21]
* CLEANUP: getRlmFitFunctions() no longer falls back to affyPLM, which
was really only needed back in 2007.
DEPRECATED AND DEFUNCT:
* CLEANUP: Dropped support for obsolete RmaPlm(..., flavor="affyPLMold").
* CLEANUP: Now RmaPlm(..., flavor="oligo") no longer supports
oligo (< 1.7.19), which can be considered obsolete version by now.
Version: 2.5.5 [2012-08-18]
* Added argument 'useTranscriptCluster' to writeCdf() for AffyGenePDInfo.
Version: 2.5.4 [2012-06-21]
* CLARIFICATION: Restructured the bpmapCluster2Cdf() method such that
is more clear how BPMAP sequences are filtered out, i.e. keeping
sequencing with a matching group name and excluding those that
appears to be non-genomic control sequences.
* ROBUSTNESS: Arguments 'rows' and 'cols' for bpmapCluster2Cdf() are
mandatory (again). The reason for this is that the BPMAP file is only
useful to infer a lower bound for them, but not their exact values.
* Added argument 'path' to bpmapCluster2Cdf(), which now defaults to
annotationData/chipTypes/<chipType>/.
BUG FIXES:
* bpmapCluster2Cdf() would exclude all units that had a probe starting at
the very first position of a BPMAP sequence, because it interpreted that
(incorrectly) as being a non-genomic control sequence. This made no
difference on some tiling arrays, but for others it dropped almost
everything in the BPMAP file, e.g. Dm_tiling2_MR_v01.bpmap. Thanks
Hanat T, Heidelberg for reporting.
* bpmapCluster2Cdf(..., minNbrOfProbes=n) filtered out units with less than
(n+2L) probes, not n probes as documented.
* bpmapCluster2Cdf() would write the incorrect 'unitnumber' in the CDF units
(it was using the BPMAP sequence index). This bug should have no impact
on analysis in the Aroma framework, because that CDF field is ignored.
Version: 2.5.3 [2012-06-18]
* FIX: Fixed a typo in an error message generated by byChipType()
for AromaChipTypeAnnotationFile.
Version: 2.5.2 [2012-06-15]
* Now writeCdf() for AffyGenePDInfo returns the pathname of the CDF.
* Added trial version of class AffymetrixPgfFile.
SOFTWARE QUALITY:
* ROBUSTNESS: Added a full system test for CalMaTe.
Version: 2.5.1 [2012-03-28]
* Now convertToUnique() for AffymetrixCelSet skips already processed
files in partially processed data sets. Previously it would give
an error if only some output files existed.
Version: 2.5.0 [2012-03-25]
* Submitted to CRAN.
SOFTWARE QUALITY:
* The package passes all redundancy tests.
Version: 2.4.3 [2012-03-23]
* CRAN POLICY: Package no longer utilizes .Internal() calls.
DEPRECATED AND DEFUNCT:
* CLEANUP: Deprecated PdInfo2Cdf() in favor (identical) pdInfo2Cdf(),
because the former does not follow the Aroma naming conventions.
Version: 2.4.2 [2012-03-06]
* GENERALIZATION: The new ArrayExplorer v3.4 will work with most
commonly used web browsers including Mozilla Firefox, Google Chrome,
Microsoft Internet Explorer, Apple Safari, and Opera.
* CRAN POLICY: Started to remove .Internal() calls.
Version: 2.4.1 [2012-01-14]
* ROBUSTNESS: Now the fit function of MbeiPlm gives an error
whenever one tries to use prior parameters, which are yet
not supported.
* Updated getFitUnitGroupFunction() for RmaPlm to support prior
probe-affinity parameters.