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.
To do that, first download the easyRNASeq package from Bioconductor: http://www.bioconductor.org/packages...asyRNASeq.html
Then unzip it
Edit the file easyRNASeq-normalize.R under R folder.
Find the following code:
Modify the above code into below:
Save the file and reinstall the easyRNASeq package with (u might need root to do so)
Rerun the R code you are able to see the normalized value.
==============================================
PHDcell: the best online free reference manager
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))]
Code:
wget http://www.bioconductor.org/packages/2.12/bioc/src/contrib/easyRNASeq_1.6.0.tar.gz
Code:
tar zxvf easyRNASeq_1.6.0.tar.gz
Find the following code:
Code:
libSizes <- librarySize(obj) libSizes <- libSizes[match(colnames(mCounts),names(libSizes))]
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))]
Code:
R CMD INSTALL easyRNASeq
==============================================
PHDcell: the best online free reference manager