error in makeVectorsAffyBatch of frmaTools package
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Ty Thomson ▴ 100
@ty-thomson-5919
Last seen 7.7 years ago
United States
Hi Matt (or anyone else who might be able to help), I get an error when trying to run the makeVectorsAffyBatch() function in the frmaTools package. I tried with an alternative cdf and I get the same error. Any ideas? Thanks! Ty > require(frmaTools) > files <- dir() > x <- makeVectorsAffyBatch(files=files, + batch.id=rep(1:3,each=3)) 1 reading GSM560669.CEL ...instantiating an AffyBatch (intensity a 506944x9 matrix)...done. Reading in : GSM560669.CEL Reading in : GSM560670.CEL Reading in : GSM560672.CEL Reading in : GSM560675.CEL Reading in : GSM560693.CEL Reading in : GSM560712.CEL Reading in : GSM560716.CEL Reading in : GSM560724.CEL Reading in : GSM560725.CEL Data loaded Attaching package: 'hgu133acdf' The following object(s) are masked from 'package:hgu133ahsentrezgcdf': i2xy, xy2i Background Corrected Error in function (classes, fdef, mtable) : unable to find an inherited method for function 'pm' for signature '"AffyBatch"' > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133acdf_2.11.0 hgu133ahsentrezgcdf_16.0.0 AnnotationDbi_1.20.7 frmaTools_1.10.0 [5] mclust_4.1 SCAN.UPC_1.0.0 Biostrings_2.26.3 IRanges_1.16.6 [9] oligo_1.22.0 oligoClasses_1.20.0 frma_1.10.0 simpleaffy_2.34.0 [13] gcrma_2.30.0 genefilter_1.40.0 affyio_1.26.0 affy_1.36.1 [17] Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affxparser_1.30.2 annotate_1.36.0 BiocInstaller_1.8.3 bit_1.1-10 codetools_0.2-8 [6] DBI_0.2-6 ff_2.2-11 foreach_1.4.0 GenomicRanges_1.10.7 iterators_1.0.6 [11] MASS_7.3-23 parallel_2.15.2 preprocessCore_1.20.0 RSQLite_0.11.3 splines_2.15.2 [16] stats4_2.15.2 survival_2.37-4 tools_2.15.2 XML_3.96-1.1 xtable_1.7-1 [21] zlibbioc_1.4.0 [[alternative HTML version deleted]]
cdf frmaTools cdf frmaTools • 869 views
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@matthew-mccall-4459
Last seen 3.7 years ago
United States
Ty, This may be a version issue -- you have frmaTools_1.10.0 installed. The latest release version is 1.12.0 and the latest devel is 1.13.0. There should definitely be a pm method for AffyBatch objects. Best, Matt On Fri, Jun 21, 2013 at 1:28 PM, Ty Thomson <tthomson at="" selventa.com=""> wrote: > Hi Matt (or anyone else who might be able to help), > > > > I get an error when trying to run the makeVectorsAffyBatch() function in the > frmaTools package. I tried with an alternative cdf and I get the same > error. Any ideas? Thanks! > > > > Ty > > > > > >> require(frmaTools) > >> files <- dir() > >> x <- makeVectorsAffyBatch(files=files, > > + batch.id=rep(1:3,each=3)) > > 1 reading GSM560669.CEL ...instantiating an AffyBatch (intensity a 506944x9 > matrix)...done. > > Reading in : GSM560669.CEL > > Reading in : GSM560670.CEL > > Reading in : GSM560672.CEL > > Reading in : GSM560675.CEL > > Reading in : GSM560693.CEL > > Reading in : GSM560712.CEL > > Reading in : GSM560716.CEL > > Reading in : GSM560724.CEL > > Reading in : GSM560725.CEL > > Data loaded > > > > > > > > Attaching package: ?hgu133acdf? > > > > The following object(s) are masked from ?package:hgu133ahsentrezgcdf?: > > > > i2xy, xy2i > > > > Background Corrected > > > > Error in function (classes, fdef, mtable) : > > unable to find an inherited method for function ?pm? for signature > ?"AffyBatch"? > > > >> sessionInfo() > > R version 2.15.2 (2012-10-26) > > Platform: x86_64-w64-mingw32/x64 (64-bit) > > > > locale: > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > > [5] LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] hgu133acdf_2.11.0 hgu133ahsentrezgcdf_16.0.0 > AnnotationDbi_1.20.7 frmaTools_1.10.0 > > [5] mclust_4.1 SCAN.UPC_1.0.0 Biostrings_2.26.3 > IRanges_1.16.6 > > [9] oligo_1.22.0 oligoClasses_1.20.0 frma_1.10.0 > simpleaffy_2.34.0 > > [13] gcrma_2.30.0 genefilter_1.40.0 affyio_1.26.0 > affy_1.36.1 > > [17] Biobase_2.18.0 BiocGenerics_0.4.0 > > > > loaded via a namespace (and not attached): > > [1] affxparser_1.30.2 annotate_1.36.0 BiocInstaller_1.8.3 > bit_1.1-10 codetools_0.2-8 > > [6] DBI_0.2-6 ff_2.2-11 foreach_1.4.0 > GenomicRanges_1.10.7 iterators_1.0.6 > > [11] MASS_7.3-23 parallel_2.15.2 preprocessCore_1.20.0 > RSQLite_0.11.3 splines_2.15.2 > > [16] stats4_2.15.2 survival_2.37-4 tools_2.15.2 > XML_3.96-1.1 xtable_1.7-1 > > [21] zlibbioc_1.4.0 > > -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880
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Hi Matt, Updating to frmaTools_1.12.0 solved my problem. Thanks! Ty -----Original Message----- From: Matthew McCall [mailto:mccallm@gmail.com] Sent: Sunday, June 23, 2013 7:55 PM To: Ty Thomson Cc: bioconductor at r-project.org Subject: Re: error in makeVectorsAffyBatch of frmaTools package Ty, This may be a version issue -- you have frmaTools_1.10.0 installed. The latest release version is 1.12.0 and the latest devel is 1.13.0. There should definitely be a pm method for AffyBatch objects. Best, Matt On Fri, Jun 21, 2013 at 1:28 PM, Ty Thomson <tthomson at="" selventa.com=""> wrote: > Hi Matt (or anyone else who might be able to help), > > > > I get an error when trying to run the makeVectorsAffyBatch() function > in the frmaTools package. I tried with an alternative cdf and I get > the same error. Any ideas? Thanks! > > > > Ty > > > > > >> require(frmaTools) > >> files <- dir() > >> x <- makeVectorsAffyBatch(files=files, > > + batch.id=rep(1:3,each=3)) > > 1 reading GSM560669.CEL ...instantiating an AffyBatch (intensity a > 506944x9 matrix)...done. > > Reading in : GSM560669.CEL > > Reading in : GSM560670.CEL > > Reading in : GSM560672.CEL > > Reading in : GSM560675.CEL > > Reading in : GSM560693.CEL > > Reading in : GSM560712.CEL > > Reading in : GSM560716.CEL > > Reading in : GSM560724.CEL > > Reading in : GSM560725.CEL > > Data loaded > > > > > > > > Attaching package: 'hgu133acdf' > > > > The following object(s) are masked from 'package:hgu133ahsentrezgcdf': > > > > i2xy, xy2i > > > > Background Corrected > > > > Error in function (classes, fdef, mtable) : > > unable to find an inherited method for function 'pm' for signature > '"AffyBatch"' > > > >> sessionInfo() > > R version 2.15.2 (2012-10-26) > > Platform: x86_64-w64-mingw32/x64 (64-bit) > > > > locale: > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > > [5] LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] hgu133acdf_2.11.0 hgu133ahsentrezgcdf_16.0.0 > AnnotationDbi_1.20.7 frmaTools_1.10.0 > > [5] mclust_4.1 SCAN.UPC_1.0.0 Biostrings_2.26.3 > IRanges_1.16.6 > > [9] oligo_1.22.0 oligoClasses_1.20.0 frma_1.10.0 > simpleaffy_2.34.0 > > [13] gcrma_2.30.0 genefilter_1.40.0 affyio_1.26.0 > affy_1.36.1 > > [17] Biobase_2.18.0 BiocGenerics_0.4.0 > > > > loaded via a namespace (and not attached): > > [1] affxparser_1.30.2 annotate_1.36.0 BiocInstaller_1.8.3 > bit_1.1-10 codetools_0.2-8 > > [6] DBI_0.2-6 ff_2.2-11 foreach_1.4.0 > GenomicRanges_1.10.7 iterators_1.0.6 > > [11] MASS_7.3-23 parallel_2.15.2 preprocessCore_1.20.0 > RSQLite_0.11.3 splines_2.15.2 > > [16] stats4_2.15.2 survival_2.37-4 tools_2.15.2 > XML_3.96-1.1 xtable_1.7-1 > > [21] zlibbioc_1.4.0 > > -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880
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