Hello,
I am computing a differential analysis on count data per region with DESeq2. For example, comparing only the region close to the transcription initiation site. Therefore, my count table represents the counts for each gene that map within a given interval (e.g. [TSS, TSS + 300]) for each sample.
I wonder if it is correct to compute the size factors with counts in the complete interval ([TSS, pA]) and then using them for the differential analysis limited in the region mentioned above. I would provide the size factors rather than calling estimateSizeFactors() with the data in my interval.
Thanks in advance for any insights
Thank you very much. This solved the issue. The MA plot helped to point me to the right size factors. Thanks again