using cuffdiff files as an input for noiseq/edge r

[4galaxy7]

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!