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 H?yer 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, >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793