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Old 05-03-2013, 07:26 AM   #1
weasteam
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Location: FL

Join Date: Dec 2008
Posts: 26
Default Solution for easyRNASeq RPKM value = NA

I was having problems in generate the rpkm values from easyRNASeq, everything I got is "NA".

The problem is because the easyRNASeq could not calculate the total reads from one bam file. The libSizes generated from the below code is "NA". It looks like the column names of the read table is bam file name, but the name of libSizes is the bam file name with absolute file address. Remove the additional filesDirectory, the problem will be solved.

Code:
libSizes <- libSizes[match(colnames(mCounts),names(libSizes))]
To do that, first download the easyRNASeq package from Bioconductor: http://www.bioconductor.org/packages...asyRNASeq.html
Code:
wget http://www.bioconductor.org/packages/2.12/bioc/src/contrib/easyRNASeq_1.6.0.tar.gz
Then unzip it
Code:
tar zxvf easyRNASeq_1.6.0.tar.gz
Edit the file easyRNASeq-normalize.R under R folder.
Find the following code:
Code:
libSizes <- librarySize(obj)
libSizes <- libSizes[match(colnames(mCounts),names(libSizes))]
Modify the above code into below:

Code:
libSizes <- librarySize(obj)
#insert these code
libSizeName=names(libSizes)
for (i in 1:length(libSizeName)){
     tmp=unlist(strsplit(libSizeName[i],"/"))
     libSizeName[i]=tmp[length(tmp)]
}
names(libSizes) = libSizeName

libSizes <- libSizes[match(colnames(mCounts),names(libSizes))]
Save the file and reinstall the easyRNASeq package with (u might need root to do so)
Code:
R CMD INSTALL easyRNASeq
Rerun the R code you are able to see the normalized value.



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