Question: A Question About Cuffdiff "Values"
0
Elwood Linney • 180 wrote:
Hello:
I am a Galaxy-naive molecular, developmental biologist studying
repression/derepression of early embryonic gene expression in
zebrafish
embryos.
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
repressed.
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
ADD COMMENT
• link
•
modified 6.3 years ago
by
Jeremy Goecks • 2.2k
•
written
6.3 years ago by
Elwood Linney • 180
