p-value and fold change

[renuka22]

Hello,

I got my rna-seq analysis from the company and they have assigned p-value to each gene. Is it possible to have a p-value from only one set of data since I had sent only one batch and there were no replicates? Also, some of my genes have p>0.05 (not differentially expressed) but high fold-change increase. So which of the two should be considered important - p-value or fold change?

Thanks

[dpryan]

If you only sent them single samples from your groups then the p-values are largely meaningless. There's not a direct correspondence between fold-change and p-value, since lowly expressed genes will randomly show higher fold-changes (i.e., the p-value is a function of expression level and fold change).

[renuka22]

Ok. But can the p-value be between my control and treatment samples as this is what they mentioned in their analysis and p<0.05 means those genes are differentially expressed?

Thanks

[dpryan]

The presumption is that the p-value is from a poisson test, so yes it's between the two samples.

Yes, p<0.05 would normally mean differentially expressed, aside from the fact that the p-values in your case are largely meaningless.

[renuka22]

So I guess the p-value is between technical replicates hence meaningless. Thanks a lot!