I have a data set generated from 88 samples in a single run using all 8 flow cells. All libraries were mixed together and sequenced on all the flow cells at a time.
So Basically I received 8 fastq files corresponding to each sample. I merged all 8 files for each sample and created single fastq file per sample.
My question is, is it necessary to look at the batch effect in this situation? if yes how shall I specify batch when I am using SVA package? If you have any other suggestion, that's also welcome.