This recently reply from Jeremy covers many of the same topics and will
likely be helpful.
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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