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

Mon Feb 6 18:00:04 CET 2012

On 02/06/2012 07:35 AM, James W. MacDonald wrote:
> 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.

The packages asprgdtua520520fcdf, asprgdtua520520fprobe are not 
Bioconductor, and seem like a likely source of problems, so you will 
want to make sure that these (a) have not changed unexpectedly and (b) 
are available to people like Jim. Martin

>
> 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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>

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