I am looking for an answer..Maybe easy for some of you! I have 2 RnaSeq datasets processed in the same way (same individual, same RNA extraction, cDNA prep and sequencing platform) the only difference is that I ran the 2 datasets on 2 separate lanes. The samples have been multiplexed and have a similar sequencing depth (# of reads). What I am trying to do is to run a gene expression analysis on them. Basically I did map both datasets against a reference transcriptome (previously generated) and I am using the raw count as EdgeR data to run the statistics. My question is...How do I account of the lane difference? Is there a way of quantifying it? Or...does the TMM normalization includes the possible lane error?
Thanks for the help!