rna seq batch effects and cross species study
hi
I am doing an expression analysis of rna seq dataset I have some doubts to be clarified
-
can we do an analysis by choosing controls and test from two different datasets?
-
One of the rna seq dataset is human(test is taken) and the other (control )is rat .is it possible to do differential expression this way?
-
In total I have three datasets for expression analysis. I did PCA before which I removed batch effects in deseq2.is it enough to remove the batch effect?..or should I do anything more ?
please do help
• 21 views
can we do an analysis by choosing controls and test from two different datasets?
No.
One of the rna seq dataset is human(test is taken) and the other (control )is rat .is it possible to do differential expression this way?
I do not see how this makes sense. The number of differential genes just by the species different (even if you manage to normalize the homologs) will overwhelm this, regardless of the treatment.
Look, there is no magic way around a proper study design. If you want to compare treatment vs control in a proper and unbiased manner then get a model (cell lines, mice, flies, rats), expose it to the treatment and control, and then assay the specimen.
Login before adding your answer.
Traffic: 2538 users visited in the last hour
Read more here: Source link
