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Last seen 10.5 years ago
Hello list,
Im having a rather strange issue here. I have a set of microarray
samples (226) collected from GEO from different studies on the same
platform (pd.mogene.1.0.st.v1). My intention is to read CEL files all
together and then divide the GeneFeatureSet in smaller objects
corresponding to the different studies. Somehow though, im able to do
that only in linux environment with R 3.0.0 while if i try on windows
with R 3.0.2 it throws me the following error when i try to subset the
GeneFeatureSet object:
library(oligo)
pd<- read.table("pd.txt", header=T)
rownames(pd)<- pd$EXACT_CEL_FILES
RawData<- read.celfiles(rownames(pd))
pda<- as(pd, "AnnotatedDataFrame")
phenoData(RawData)<- pda
studiesID<- levels(RawData$Study)
for(i in 1:length(studiesID)){
d<-studiesID[i]
assign(d, RawData[,pData(RawData)$Study == studiesID[i]])
}
Error in `$<-.data.frame`(`*tmp*`, "channel", value = integer(0)) :
replacement has 0 rows, data has 7
I attach both the sessionInfo for Linux and Windows.
Thank you very much!
-- output of sessionInfo():
> sessionInfo() [LINUX]
R version 3.0.0 (2013-04-03)
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] pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.4
[3] DBI_0.2-7 oligo_1.24.2
[5] Biobase_2.20.1 oligoClasses_1.22.0
[7] BiocGenerics_0.6.0
loaded via a namespace (and not attached):
[1] affxparser_1.32.3 affyio_1.28.0 BiocInstaller_1.10.4
[4] Biostrings_2.28.0 bit_1.1-12 codetools_0.2-8
[7] ff_2.2-13 foreach_1.4.2 GenomicRanges_1.12.5
[10] IRanges_1.18.3 iterators_1.0.7 preprocessCore_1.22.0
[13] splines_3.0.0 stats4_3.0.0 tools_3.0.0
[16] zlibbioc_1.6.0
> sessionInfo() [WINDOWS]
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C LC_TIME=English_United
Kingdom.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.4 DBI_0.2-7
oligo_1.26.6 Biostrings_2.30.1
[6] XVector_0.2.0 IRanges_1.20.7
Biobase_2.22.0 oligoClasses_1.24.0 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] affxparser_1.34.2 affyio_1.30.0 BiocInstaller_1.12.1
bit_1.1-12 codetools_0.2-8 ff_2.2-13
[7] foreach_1.4.2 GenomicRanges_1.14.4 iterators_1.0.7
preprocessCore_1.24.0 splines_3.0.2 stats4_3.0.2
[13] tools_3.0.2 zlibbioc_1.8.0
--
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