Statistic on FPKMs of gene in one condition

[Renshin]

Hello,

With the help of cufflinks; I calculated the number of FPKM for each contigs. In my study, I don't want to know which genes are expressed differently according to the conditions. I just want to know which ones are the most expressed. What program can I use or statistic?

Thank you for you help

[dpryan]

If you already have FPKMs then you already have your answer. The FPKM is the metric, just use the highest X%.

[Renshin]

I have perhaps statistically classify the FPKMs , it could be interesting. No ?

[dpryan]

You can use a method like zFPKM if you need something other than top X%, but that's not what you mentioned in your first post.

[Renshin]

Thank you, very interesting. I'm researching of ideas for my study on the FPKMs. I'm open to ideas.

[Renshin]

I calculated the zFPKM, but I don't calculate the treshold because I don't have a file containing the results of chromatin state analysis. Moreover, i work about an insect, i can't use threshold de -3 for human.

Can you help me