Hi, all; I encountered the following error while using makeVectorsAffyBatch() function in frmaTools library on 141 Affymetrix HG-U133 Plus 2 chips (single batch). abatch.ref <- makeVectorsAffyBatch(files.ref, rep(1,length(files.ref)), file.dir=FILED) 1 reading GSM493958.CEL ...instantiating an AffyBatch (intensity a 1354896x141 matrix)...done. Reading in : GSM493958.CEL Reading in : GSM493960.CEL Reading in : GSM493965.CEL Reading in : GSM493966.CEL Reading in : GSM493970.CEL Reading in : GSM494235.CEL Reading in : GSM494237.CEL Reading in : GSM494240.CEL Data loaded Background Corrected Normalized Beginning Probe Effect Calculation ... Finished probeset: 1000 Finished probeset: 2000 Finished probeset: 3000 Finished probeset: 4000 Finished probeset: 53000 Finished probeset: 54000 Probe Effects Calculated Probe Variances Calculated Probe Set SDs Calculated Beginning Median SE Calculation ... Error in if (any(w < 0)) { : missing value where TRUE/FALSE needed Any suggestion? I ran the code under following environment: > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133plus2cdf_2.11.0 AnnotationDbi_1.20.7 frmaTools_1.10.0 [4] frma_1.10.0 affy_1.36.1 Biobase_2.18.0 [7] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] BiocInstaller_1.8.3 Biostrings_2.26.3 DBI_0.2-5 [4] GenomicRanges_1.10.7 IRanges_1.16.6 MASS_7.3-23 [7] RSQLite_0.11.2 affxparser_1.30.2 affyio_1.26.0 [10] bit_1.1-10 codetools_0.2-8 ff_2.2-11 [13] foreach_1.4.0 iterators_1.0.6 oligo_1.22.0 [16] oligoClasses_1.20.0 parallel_2.15.2 preprocessCore_1.20.0 [19] splines_2.15.2 stats4_2.15.2 tools_2.15.2 [22] zlibbioc_1.4.0 Thanks in advance, TH -- Tae-Hoon Chung, PhD [[alternative HTML version deleted]]

The issue is that you are trying to estimate between-batch residual variances with only 1 batch: abatch.ref <- makeVectorsAffyBatch(files.ref, rep(1,length(files.ref)), file.dir=FILED) I'm curious why you are making your own fRMA vectors. HGU133plus2 has pre-made frozen parameter vectors in the hgu133plus2frmavecs package, so you could use those to preprocess your data. Best, Matt On Fri, May 31, 2013 at 2:40 AM, Tae-Hoon Chung <hoontaechung at="" gmail.com=""> wrote: > Hi, all; > > I encountered the following error while using makeVectorsAffyBatch() > function in frmaTools library on 141 Affymetrix HG-U133 Plus 2 chips > (single batch). > > > abatch.ref <- makeVectorsAffyBatch(files.ref, rep(1,length(files.ref)), > file.dir=FILED) > 1 reading GSM493958.CEL ...instantiating an AffyBatch (intensity a > 1354896x141 matrix)...done. > Reading in : GSM493958.CEL > Reading in : GSM493960.CEL > Reading in : GSM493965.CEL > Reading in : GSM493966.CEL > Reading in : GSM493970.CEL > > ? > > Reading in : GSM494235.CEL > Reading in : GSM494237.CEL > Reading in : GSM494240.CEL > Data loaded > > Background Corrected > > Normalized > > Beginning Probe Effect Calculation ... > > Finished probeset: 1000 > > Finished probeset: 2000 > > Finished probeset: 3000 > > Finished probeset: 4000 > > ? > > Finished probeset: 53000 > > Finished probeset: 54000 > > Probe Effects Calculated > > Probe Variances Calculated > > Probe Set SDs Calculated > > Beginning Median SE Calculation ... > > Error in if (any(w < 0)) { : missing value where TRUE/FALSE needed > > > Any suggestion? > I ran the code under following environment: > > >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu133plus2cdf_2.11.0 AnnotationDbi_1.20.7 frmaTools_1.10.0 > [4] frma_1.10.0 affy_1.36.1 Biobase_2.18.0 > [7] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] BiocInstaller_1.8.3 Biostrings_2.26.3 DBI_0.2-5 > [4] GenomicRanges_1.10.7 IRanges_1.16.6 MASS_7.3-23 > [7] RSQLite_0.11.2 affxparser_1.30.2 affyio_1.26.0 > [10] bit_1.1-10 codetools_0.2-8 ff_2.2-11 > [13] foreach_1.4.0 iterators_1.0.6 oligo_1.22.0 > [16] oligoClasses_1.20.0 parallel_2.15.2 preprocessCore_1.20.0 > [19] splines_2.15.2 stats4_2.15.2 tools_2.15.2 > [22] zlibbioc_1.4.0 > > Thanks in advance, > > TH > > > -- > Tae-Hoon Chung, PhD > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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 -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880