How to analyse normalized read count?

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9.5 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.

RNA-Seq R • 5.7k views

ADD COMMENT • link updated 23 months ago by Ram 44k • written 9.5 years ago by pbio ▴ 150

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Are you really sure you want to use house keeping genes for normalization? That's not exactly the most robust method.

ADD REPLY • link 9.5 years ago by Devon Ryan 104k

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How do you address the problem of variability in data coming from different centers?

ADD REPLY • link 9.5 years ago by pbio ▴ 150

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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.