error when running makeVectorsAffyBatch
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Loraine, Ann ▴ 50
@loraine-ann-5437
Last seen 8.4 years ago
Hello, I am trying to use makeVectorsAffyBatch from frmaTools to make vectors suitable for processing ATH1/GPL198 Affymetrix microarrays. However, I'm getting this error message printed to the console: "Probe Set SDs Calculated Beginning Median SE Calculation ... Error in if (any(w < 0)) { : missing value where TRUE/FALSE needed" The code is: library(frmaTools) f='data/cels4frmatools_inputs.tsv' d=read.delim(f,sep='\t',header=T,as.is=T) files=sapply(list(d$cel),function(x){paste0('CEL/',x)}) batches=d$num ath1=makeVectorsAffyBatch(files[500],batches[500]) > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] ath1121501cdf_2.12.0 AnnotationDbi_1.22.6 frmaTools_1.12.0 [4] affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] affyio_1.28.0 BiocInstaller_1.10.4 DBI_0.2-7 [4] IRanges_1.18.4 preprocessCore_1.22.0 RSQLite_0.11.4 [7] stats4_3.0.1 tools_3.0.1 zlibbioc_1.6.0 files and batches: > files[1:10] [1] "CEL/GSM1009026_Col_luc_AA_1_ATH1.CEL.gz" [2] "CEL/GSM1009031_Col_luc_H2O2_3_ATH1.CEL.gz" [3] "CEL/GSM1009035_rao2-1_AA_1_ATH1.CEL.gz" [4] "CEL/GSM1009038_rao2-1_H2O2_1_ATH1.CEL.gz" [5] "CEL/GSM1009042_rao2-1_water_2_ATH1.CEL.gz" [6] "CEL/GSM1009049_TDNA1_H2O2_3_ATH1.CEL.gz" [7] "CEL/GSM1009054_TDNA2_AA_2_ATH1.CEL.gz" [8] "CEL/GSM1009055_TDNA2_AA_3_ATH1.CEL.gz" [9] "CEL/GSM1009057_TDNA2_H2O2_2_ATH1.CEL.gz" [10] "CEL/GSM1009060_TDNA2_water_2_ATH1.CEL.gz" > batches[1:10] [1] 221 221 221 221 221 221 221 221 221 221 Can you tell from this what I am doing wrong? Best, Ann ------------------------------- Ann Loraine, Ph.D. Associate Professor Department of Bioinformatics and Genomics University of North Carolina at Charlotte North Carolina Research Campus 600 Laureate Way Kannapolis, NC 28081 704-250-5750 aloraine@uncc.edu http://www.transvar.org http://www.bioviz.org http://www.uncc.edu [[alternative HTML version deleted]]
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