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: 

> 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 

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,
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