using cuffdiff files as an input for noiseq/edge r

4galaxy7 · 12-02-2015, 02:32 AM

hi,

i've put all my samples through cuffdiff (3 treatments, 7 samples in each treatment) and i also want to find differentially expressed genes from noiseq and edge r. I was struggling a bit with converting the folders that cuffdiff produces into a format for edge r and noiseq

for instance, it says on this https://www.bioconductor.org/package...doc/NOISeq.pdf that you need your samples ordered, such that each column is a sample and each row is a gene/locus. there doesn't seem to be any cuffdiff output which corresponds to this and i dont really know enough perl to write a script which would convert them to one. Can anyone give me some advice on how to turn the right format?

Thanks!

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12-02-2015, 02:32 AM	#1
4galaxy7 Member Location: UK Join Date: Nov 2015 Posts: 19	using cuffdiff files as an input for noiseq/edge r hi, i've put all my samples through cuffdiff (3 treatments, 7 samples in each treatment) and i also want to find differentially expressed genes from noiseq and edge r. I was struggling a bit with converting the folders that cuffdiff produces into a format for edge r and noiseq for instance, it says on this https://www.bioconductor.org/package...doc/NOISeq.pdf that you need your samples ordered, such that each column is a sample and each row is a gene/locus. there doesn't seem to be any cuffdiff output which corresponds to this and i dont really know enough perl to write a script which would convert them to one. Can anyone give me some advice on how to turn the right format? Thanks!