Hi El,
> 1) what do these numbers represent?
FPKM values for sample 1 and 2. Cufflinks documentation is the place to get
definitions for all columns:
http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff
> 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
These questions get at the challenge of interpreting FPKM values. One thing to
look at is the confidence intervals (CI) produced by Cufflinks/diff. CIs that
overlap 0 are, in my experience, unreliable no matter how large the FPKM.
Most likely genes with FPKM values near 0 have CIs overlapping 0, which means
there's likely no difference between them. However, genes with low FPKM values
( e.g. < 10) but tight CIs and > 0 should probably be included for further
analysis.
Another thing to look at is whether a couple highly-expressed genes are
reducing FPKM values. If so, using the upper-quartile normalization option can
help you get better resolution for genes expressed at low levels.
Good luck,
J.
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