Entering edit mode
7.8 years ago
pbio ▴ 150
I have read counts for two samples coming from different data center, which are normalized using house keeping genes and got the relative expression for each gene samples. Is there any R package to calculate differential expressed genes between two samples using normalized read counts?
I know DESeq and EdgeR, but these packages takes the read counts and do the normalization but not the normalized read counts.
Please let me know any R package for working with normalized read counts.
Thanks in advance.
Are you really sure you want to use house keeping genes for normalization? That's not exactly the most robust method.
How do you address the problem of variability in data coming from different centers?
If group A was sequenced at center X and group B at center Y then there's no good way to compare A and B. There are ways to get around that, but it's easier to just do the experiment properly than to try to account for everything post-hoc. If you really only have 2 samples, then you'll never be able to draw very meaningful results regardless of the method.
Yep ... got it thanks Devon..