I have two
RNAseq data with 4 different treatments run in 2017 (Let's say treatment A and B) and 2019 (Treatment C and D); those have two different read lengths (I read for DE it does not matter the read length). For every experiment I have
treated vs untreated. So I have 2 questions:
Is it better to create one single
ddsobject for all
RNAseqexperiments and then compare whatever I want using
DESeq2 contrastoption, or separate
ddsobjects for each contrast group. I have tried to experiment a bit and I get different number of genes. Why is that and which method is more precise?.
should I test
treated vs untreated, or
untreated vs treated? Also in this case i get inverse number of
up/down regulated genes. Ie. In case of
treated vs untreatedI get more
down-regulated genesand in case of
untreated vs treatedI get more
up-regulated genes. I took one gene and controlled that its up/down regulation depends on this.