I am a Galaxy-naive molecular, developmental biologist studying
repression/derepression of early embryonic gene expression in zebrafish

After attending the Galaxy meeting I returned home and worked up two
mRNAseq files to determine RNA expression differences using cuffdiff
between a treated and an untreated sample (i.e. data from cuffdiff under
the title of "gene differential expression testing").

I downloaded the data, opened it up in an Excel file and captured all the
"significant" rows.

If I look at the "value 1" and "value 2" columns I find that many of the
numbers are single digits.  I expect that in one of the columns that the
numbers will be very low (that is, less than 1) because the treatment
should be inducing gene expression in a subfamily of genes that are

My questions are:

1) what do these numbers represent?

2) If in the "value" column where I expect a higher number has  a "value of
10" or less mean anything or should one be selecting for values higher that
these single digit numbers

3) And in the column of genes that might be repressed is there really a
difference between a "value of 0.1  versus something like 0.01" since that
can change my log ratios significantly--this, of course, goes back to my
first question

I would appreciate any help I could get, sincerely,

el linney
Professor of Molecular Genetics and Microbiology
Duke University Medical Center
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