What kind of statistics to use to compare logFold values?

Question

[Patricia]

Hi everyone,

I recently did an RNAseq experiment in which I had controls and experiments at 3 different time periods. My samples were distributed as following for a total of 10 samples:

T1_control1, T2_control1, T2_control2, T3_control1,

T1_exp1, T1_exp2, T2_exp1, T2_exp2, T3_exp1, T3_exp2

I did differential expression analysis with DESeq2 and from it I obtained 3 files from each time period T1, T2, and T3 that show the logFold change values from the control to the experimental for each gene. My question is how I can statistically compare the logFold change value for one gene in one period vs another time period. I am not sure what test to use since there is only one logFold change values per each time period for each gene.

Thank you in advance.

Answer 1

[Istvan Albert]

to compare over time periods, you will need to build a statistical model that represents the question that you want to ask

then the FDR value that you get reflects the assumptions of the model

to test just two time points relative to one another, you can run a pairwise comparison between those two samples

but in general, you should build a model like described here:

https://hbctraining.github.io/DGE_workshop_salmon_online/lessons/08b_time_course_analyses.html

and more practical examples here

https://support.bioconductor.org/p/99730/

[Patricia]

Thank you for the help!

Answer 2

[swbarnes2]

I think what you are trying to do is to see if T1/conrtol log fold changes are different from T2/control changes.

Just compare T1 to T2 directly. If they are different, they are different. Adding the inherent variability of the control samples isn't going to make the picture clearer.

[Patricia]

Right, I can see that they are different but I would like to know if there is a way to tell if this difference is significant or not.

[Istvan Albert]

the tool that generated the fold changes also computes and provides that information in the adjusted value column