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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Jennifer Jackson
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