I am using DESeq2 for finding differential expressed genes.
Originally, there were around 49,000 genes in rawcount of expression, however, when I performed these steps, the number of genes were almost half of rawcount.
ddsk14 <- estimateSizeFactors(ddsk14) sizeFactors(dds_k14)
K14CTRL1 K14CTRL2 K14Exp1 K14Exp2 1.0163136 1.0524673 0.9809502 0.9752045
View(counts(dds_k14, normalized = TRUE))
I tried to understand why the genes are filtered out on normalization step, it was hard to grab with the paper and vignettes. Could you explain to me a little bit easier way about this?
Thanks in advance!