[BioC] Updated affy package? ReadAffy/ AffyBatch has changed and breaks my pipeline!

Mon Feb 6 16:35:50 CET 2012

Hi Benjamin,

You need to supply us with a small reproducible example of the problem 
you are experiencing, so we can either track down the error, or explain 
how you can fix things on your end.

Best,

Jim

On 2/6/2012 7:43 AM, Benjamin Høyer wrote:
> Hi
>
> I have made a pipeline for automating analysis of custom affymetrix
> chips for a colleague.  After an R-update, the pipeline no longer
> runs.  Working backwards from where the error occurs, I have found
> that the structure produced by ReadAffy() is no longer the same.  I am
> using exactly the same data set.  (The error itself a failed assign()
> due to a locked binding, but I don't think that's related.)
>
> Below are the lists of packages installed before and after the update,
> with version numbers.  The 'old' R version is 2.13.2, the 'new' one is
> 2.14.1.
>
> OldPackVers<- structure(c("1.30.0", "1.20.0", "1.28.5", "1.14.1", "1.30.0",
> "0.0.1", "0.0.1", "2.13.2", "2.12.2", "2.20.4", "1.0-4.1", "1.3-2",
> "1.12", "7.3-3", "1.14.1", "0.2-8", "2.13.2", "1.6.2", "2.13.2",
> "0.2-5", "1.30.0", "1.6", "1.2.8", "0.8-48", "2.24.1", "2.8.2",
> "1.2.5", "2.10.1", "2.13.2", "2.13.2", "2.13.2", "2.6.2", "1.10.6",
> "2.23-6", "0.19-33", "3.8.3", "1.1.7", "1.30.0", "1.30.0", "7.3-14",
> "1.0-3", "2.13.2", "2.10.0", "1.7-11", "3.1-103", "7.3-1", "1.14.0",
> "3.1-51", "0.11.1", "7.3-3", "2.13.2", "2.13.2", "2.13.2", "2.36-10",
> "2.13.2", "1.24.0", "1.30.0", "2.13.2", "2.13.2", "1.30.0"), .Names = c("affy",
> "affyio", "affyPLM", "AnnotationDbi", "asprgdtua520520fcdf",
> "asprgdtua520520fprobe", "bac01a520746fprobe", "base", "Biobase",
> "Biostrings", "bitops", "boot", "caTools", "class", "cluster",
> "codetools", "compiler", "corpcor", "datasets", "DBI", "DynDoc",
> "e1071", "fdrtool", "foreign", "gcrma", "gdata", "GeneNet", "gplots",
> "graphics", "grDevices", "grid", "gtools", "IRanges", "KernSmooth",
> "lattice", "limma", "longitudinal", "makecdfenv", "marray", "MASS",
> "Matrix", "methods", "Mfuzz", "mgcv", "nlme", "nnet", "preprocessCore",
> "rpart", "RSQLite", "spatial", "splines", "stats", "stats4",
> "survival", "tcltk", "timecourse", "tkWidgets", "tools", "utils",
> "widgetTools"))
>
> NewPackVers<- structure(c("1.32.1", "1.22.0", "1.30.0", "1.16.11", "1.32.0",
> "0.0.1", "2.14.1", "2.14.0", "1.2.1", "2.22.0", "1.0-4.1", "1.3-4",
> "1.12", "7.3-3", "1.14.1", "0.2-8", "2.14.1", "1.6.2", "2.14.1",
> "0.2-5", "1.32.0", "1.6", "1.2.8", "0.8-48", "2.26.0", "2.8.2",
> "1.2.5", "2.10.1", "2.14.1", "2.14.1", "2.14.1", "2.6.2", "1.12.5",
> "2.23-7", "0.20-0", "3.10.2", "1.1.7", "1.32.0", "1.32.0", "7.3-16",
> "1.0-3", "2.14.1", "2.12.0", "1.7-13", "3.1-103", "7.3-1", "2.14.1",
> "1.16.0", "3.1-51", "0.11.1", "7.3-3", "2.14.1", "2.14.1", "2.14.1",
> "2.36-10", "2.14.1", "1.26.0", "1.32.0", "2.14.1", "2.14.1",
> "1.32.0", "1.0.0"), .Names = c("affy", "affyio", "affyPLM", "AnnotationDbi",
> "asprgdtua520520fcdf", "asprgdtua520520fprobe", "base", "Biobase",
> "BiocInstaller", "Biostrings", "bitops", "boot", "caTools", "class",
> "cluster", "codetools", "compiler", "corpcor", "datasets", "DBI",
> "DynDoc", "e1071", "fdrtool", "foreign", "gcrma", "gdata", "GeneNet",
> "gplots", "graphics", "grDevices", "grid", "gtools", "IRanges",
> "KernSmooth", "lattice", "limma", "longitudinal", "makecdfenv",
> "marray", "MASS", "Matrix", "methods", "Mfuzz", "mgcv", "nlme",
> "nnet", "parallel", "preprocessCore", "rpart", "RSQLite", "spatial",
> "splines", "stats", "stats4", "survival", "tcltk", "timecourse",
> "tkWidgets", "tools", "utils", "widgetTools", "zlibbioc"))
>
> The differences in structure are thus:
>
> datOld<- ReadAffy(celfile.path=subdircel)
> datOld
>> AffyBatch object
>> size of arrays=716x716 features (24 kb)
>> cdf=AsprgDTUa520520F (11186 affyids)
>> number of samples=27
>> number of genes=11186
>> annotation=asprgdtua520520f
>> notes=
> datNew<- ReadAffy(celfile.path=subdircel)
> datNew
>> AffyBatch object
>> size of arrays=716x716 features (15 kb)
>> cdf=AsprgDTUa520520F (11186 affyids)
>> number of samples=27
>> number of genes=11186
>> annotation=asprgdtua520520f
>> notes=
>
> The particular slot which causes trouble is phenoData;
> datOld at phenoData
>> An object of class "AnnotatedDataFrame"
>>   sampleNames: 1a_N6h_ t1.CEL, 1b_N6h_t2.CEL, ..., 9c_N192h_t3.CEL  (27 total)
>>   varLabels and varMetadata description:
>>     sample: arbitrary numbering
> datNew at phenoData
>> An object of class "AnnotatedDataFrame"
>>   sampleNames: 1a_N6h_ t1.CEL 1b_N6h_t2.CEL ... 9c_N192h_t3.CEL (27 total)
>>   varLabels: sample
>>   varMetadata: labelDescription
>
> Is this a likely culprit?  Another option could be how 'get' works.
> Basically my function 'get's the probe package name (the script
> follows Gillespie's doi:10.1186/1756-0500-3-81).  In the first case, I
> get
>
> get(probepackagename)
>> Object of class probetable data.frame with 121507 rows and 6 columns.
> And in the second case, I get:
>> Object of class probetable data.frame with 468384 rows and 6 columns.
>> First 3 rows are:
>>                     sequence x y    Probe.Set.Name Probe.Interrogation.Position
>> 1<seq1>  5 1<name1>                            13
>> 2<seq2>  6 1<name2>                            13
>> 3<seq3>  7 1<name3>                            13
>>    Target.Strandedness
>> 1           Antisense
>> 2           Antisense
>> 3           Antisense
> Basically, I would like to know what has changed in the newer versions
> that I have!  Could also be that the 'probepackagename' (which is
> generated earlier in the script) has changed.  This would be the
> result of an update in makeProbePackage() in AnnotationDbi.
>
> I'll keep looking for ways to get round it, but thanks in advance!
>
> Regards,
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

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