Solution for easyRNASeq RPKM value = NA

weasteam · 05-03-2013, 08:26 AM

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.

==============================================
PHDcell: the best online free reference manager

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Solution for easyRNASeq Error in .doBasicCount(obj)	weasteam	Bioinformatics	0	05-02-2013 03:28 PM
easyRNASeq errors / experiences	rboettcher	Bioinformatics	5	09-20-2012 09:49 AM
easyRNASeq	calmac3	RNA Sequencing	2	09-20-2012 09:46 AM
RNA-Seq: easyRNASeq: a bioconductor package for processing RNA-Seq data.	Newsbot!	Literature Watch	0	08-01-2012 03:00 AM
Does anyone have a solution	NathalieA	454 Pyrosequencing	2	05-16-2012 12:57 AM

05-03-2013, 08:26 AM	#1
weasteam Member Location: FL Join Date: Dec 2008 Posts: 26	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. ============================================== PHDcell: the best online free reference manager