Question: How To Extrapolate Differentially Expressed Genes After Running Cuffdiff?
1
gravatar for i b
5.8 years ago by
i b330
i b330 wrote:
Hi guys, have a question about the cuffdiff output "differential expression testing". For most of you might sound "naive" but I'm new to this field and I have very little background in statistic. So, I have compared a control sample with 2 biological replicates using cuffdiff. I have now about 4000 genes which were tested. 1. How do I extrapolate the genes which are up- or downregulated from the 4000? 2. Is there a FPKM value above which a gene is up- or downregulated? 3.I used excel and sorted the values from highest to smallest: assuming that control highest value is 200 and the correspondent treated values is 2, can I say that that gene is downregulated in the treated ssamples by a 100 fold chnage? 4. Do I have to use at all the p_values given in the output to extrapolate the most up- or downregualted genes? I do not have yet cummerbund and I am not very good with R. And I 'm lost! Thanks, ib
rna-seq cuffdiff • 1.4k views
ADD COMMENTlink modified 5.8 years ago by Jennifer Hillman Jackson25k • written 5.8 years ago by i b330
1
gravatar for Jennifer Hillman Jackson
5.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello IB, This recently reply from Jeremy covers many of the same topics and will likely be helpful. http://lists.bx.psu.edu/pipermail/galaxy-user/2012-August/004985.html Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD COMMENTlink written 5.8 years ago by Jennifer Hillman Jackson25k
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