NOISeq Batch Correction to RNA-seq data

Question

[endikavarela]

Hello,

I'm working with RNA-seq data with a known batch effect (samples in witch the RNA extraction method differ) and I have tried different programs to count for that effect. But the only one for now that seems to work is the function ARSyNseq from the NOISeq package seeing the PCA after correction.

Now I want to use the data corrected (ARSyNseq returns values corrected for the batch effect and in my case normalized with TMM) in a program such as EdgeR, limma or DESeq2 to find differentially expressed genes (NOISeq returns a lot of DEGs), but EdgeR and DESeq only can be input with unnormalized counts. I would like to ask to the experts from this page if there is a way to use the output from ARSyNseq in limma or another program.

Thanks.