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 On 7/29/12 3:50 PM, i b 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!

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