statistical analysis

[feng]

How to do statistical analysis on differentially expressed genes from RNA-seq?

Results as


genes Sample1 Sample2
xxxx 12 23
xxxx 155 30

Numbers stand for times of gene sequence.

[Bukowski]

How to do statistical analysis on differentially expressed genes from RNA-seq?

Results as


genes Sample1 Sample2
xxxx 12 23
xxxx 155 30

Numbers stand for times of gene sequence.

Not much chance of statistical analysis with only two samples.

I think DESeq http://www-huber.embl.de/users/anders/DESeq/ has instructions for unreplicated conditions though. If you search the forums there are plenty of discussions on SeqAnswers about this topic.

[ickou]

You can use "NOISeq-sim: no replicates"

http://bioinfo.cipf.es/noiseq/doku.php?id=tutorial