Cuffdiff - inf values

[TRA]

I ran Bowtie to align my RNA-seq of 18 samples, 3 per group, single end read sequencing. Some of LogFc values that I got from CuffDiff assigned to inf or -inf. What does that mean? Can I replace the -inf with -5 and the inf with 5 to run pathway analysis. (I substitute every positive LogFc with 5 and the negative LogFc with -5).

Any help would be appreciated

[blancha]

According to Cuffdiff, any float divided by 0 is equal to inf, and 0 divided by any float is equal to -inf.

First, filter out all the genes or isoforms below a given FPKM treshold in both conditions, e.g. 1 or 10 FPKM.
With this step, you will remove the majority of the fold changes equal to -inf or inf.

After having performed this filtering step, I think the algorithm you propose is acceptable. I follow a similar strategy, with a small variation. I just replace inf with the maximum fold change in the conditions being compared plus one, and replace -inf with the minimum fold change in the conditions being compared minus one. This algorithm is slightly better, since it is possible to have fold changes over 5. inf will always then always be higher than any reported fold change, and -inf will always be lower than any reported fold change.