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Old 03-31-2014, 12:12 PM   #61
super0925
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Location: UK

Join Date: Feb 2014
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Quote:
Originally Posted by dpryan View Post
Have a look at my answer over on biostars to a similar question. That should tell you most of what you want to know (particularly given the included links and replies from others).
Hi dpryan
If I only have one sample in each condition, how do I do the DE analysis?
Cause I think I need at least 2 replicates in each condition and then doing the DE statistical by DESeq/edgeR/Cuffdiff. Am I right?

If I don't run Cufflinks but running Htseq-counts,
Could I use this kind of method to measure it?

gene1: (a1/s1)-(a2/s2)

a1 is the counts (i.e. the number of mapped reads) of this gene in sample1
s1 is the total mapped reads in sample 1
a2 is the counts (i.e. the number of mapped reads) of this gene in sample2
s2 is the total mapped reads in sample 2

Or if I use FPKM calculated by Cifflinks to measure it ? i.e. FPKM1-FPKM2?
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