On 8/21/12 4:33 AM, i b wrote:
Thanks Jen,
useful link. But I did not understand one thing.
I have the following FPKM in cufflinks for two samples:
s1 (untreated): 1234106
s2 (treated): 159713
cuffdiff of the two samples gives me the following values:
value_1: 5.4
value_2: 20.9
and it is not significant (!). My two question:
1. how is this not significant?
2. what is the realtion between the high fpkm in cufflinks and the low
values in cuffdiff?I read the manual: is this part of the statistical
method adopted?e.g are these numbers (cuffdiff values) derived from
the formula adopted?
thanks a lot,
ib
On Thu, Aug 16, 2012 at 11:26 PM, Jennifer Jackson <j...@bx.psu.edu> wrote:
Hello,
A very similar question came up a few days ago and Jeremy had some good
advice for how to approach learning to interpret this data:
http://lists.bx.psu.edu/pipermail/galaxy-user/2012-August/004985.html
Best,
Jen
Galaxy team
On 8/15/12 8:49 AM, i b wrote:
Dear all,
in cuffdiff outputs e.g. transcript differential expression, I find for
example:
value_1 value_2 log2(fold_change)
7.77183 0 -1.79769e+308
or
value_1 value_2 log2(fold_change)
0 14.5972 1.79769e+308
for many many rows.
if I sort in excel my data by fold change column (big to small ), all
the rows with -1.79769e+308 or +1.79769e+308 are on the top.
How can be sure that these on the top are really the most up-regulated
or down regulated transcripts if I don't know the real value of one of
the two samples (is 0 really zero?)?
I was told that the zero in one if the two samples is very small
number and Cuffdiff simply writes 0, but it is not absolutely zero,
otherwise it would not be possible ot have -1.79769e+308 or
1.79769e+308
Could you please tell me then how can I extrapolate the highest fold
change? (up and down regualted)?or of what is done by sorting by log
fold chnage is correct?
Thanks,
ib
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