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Old 11-02-2010, 06:57 AM   #3
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Location: Rochester, MN

Join Date: Mar 2009
Posts: 191

Originally Posted by nkwuji View Post

Another question is, does anyone know how to set up the minimal threshold in the cuffdiff to do the test. For example, I have a gene expressed mildly in one sample (FPKM 8), but no expression in the other sample (FPKM 0). It is actually one of the most interesting genes I was looking for. But in the cuffdiff, it has the mark of "NOTEST", thus the significance is "no". Can anyone give me any help on this? Can I manually select these genes as differentially expressed genes, because they are expressed and actually the pvalue is also 0?

Plus, can I remove genes expressed in the low level manually, e.g. for genes with FPKM < 1? These genes dont look very promising...

The cuffdiff -c option might be what you are looking for
-c/--min-alignment-count <int>
This limits the differential testing based on counts - rather than FPKM. However, do you think it is wise/necessary to use this feature if what you want to say is that it is present in one condition and not the other?
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