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Old 08-30-2013, 01:58 AM   #2
Location: Berlin

Join Date: Oct 2010
Posts: 71

Hi Alex,

just to be sure: did you use Cufflink's FPKM for DESeq?

(a) Did you check the quality of these reads? Did both conditions give equal output (number of reads, quality)?

(b) You can use IGV and load the GTF file from cufflinks (maybe have to convert it to BED first)

(c) Ranking by p-value is commonly done, but I would argue that statistically speaking, ranking by FC makes more sense after applying a fixed p-value cut-off (such as 0.05 or 0.01). Then, either gene expression is significantly different between two condition or it is not, so not situation where "gene A is more significant than gene B".
rboettcher is offline   Reply With Quote