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


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