I have several different databases of RNA-seq data, in a mix of TPM, RPKM, and raw counts. I plan to convert all to TPM and then to use Voom in Limma to normalize the samples and identify DE genes. The problem is that one of the databases is paired end while the rest are single end. Is it possible to make comparisons between the different chemistries? One thing that worries me is that the PE database is from a different tissue than the rest, so I would expect the PE samples to cluster separately regardless of sequencing chemistry.
I found this post differential expression analysis-- paired-end and single-end which has given me some hope (my PE counts data is also from HTSeq). It is my understanding that Voom will remove the batch effects of the SE vs PE chemistry. Am I correct in my thinking that I can just throw everything Voom after calculating normalization factors and it will be ok? Or am I trying to do something impossible?
Any advice is appreciated,