The zero value in RNA seq

Question

[saj98]

Hello everyone

I have RNA seq FPKM, some of the genes came with zero value for treatment group, but with defined value for the control group. The cuff links read them as significant genes. Can we recognize these genes not express in treatment group but they do so in control group?

Thanks for help

[BioinfGuru]

Hi saj98 - I think it the grammar of your question is not clear - what do you mean by "Can we recognize these genes"?

[saj98]

Hello Sorry for misunderstanding, my question: can I count these genes even if their value zero in treatment group?

Thanks

[BioinfGuru]

IF fpkm>0 for gene X in control group

AND fpkm=0 for gene X in treatment group

AND p<0.05 (according to cufflinks)

THEN there is a significant difference between treated and control for gene X at the 0.05 significance level

The simple conclusion (with no other information) is that treatment has stopped the expression of gene X

[saj98]

Thank you so much, you answer was useful for me.