I've a matrix for mouse genes with length and FPKM values from 4 different cell types. I was wondering how can I go from here to finding Differentially Expressed Genes?
Which tool do you want to use: limma? DESeq?
I can use any tool. it should just be able to get me the DEGs :)
I tried DESeq, but somehow it needs integer values to add condition labels before proceeding.
DESeq is not suitable for FPKM, it wants raw counts. You might use cuffdiff.
do you know how I would go about obtaining raw counts from my RNA seq data?
Most of the packages for finding differential expression (DE) does the normalization itself. You can use the raw counts as input. There are many tools available for DE, example edgeR, DESeq etc.,
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