Best cutoff for fold change of microarray data

Question

[Calangoa]

Dear all I have 6 microarray data set and I want to select a cut off base on adj. p.value and fold change to find DEGs. About adj. p.value, I know a cut off less than .05 or .01 are the best but what is the best fold chang cutoff if we want to compare different datasets? all datasets are affymatrix and normalized base on R package.

[Calangoa]

All dataset are affymetix and normalized on GEO2R from NCBI. After that I want to select a cut off and I know it is different among veriety of data.

[GenoMax]

nfs.falsafi : Please do not delete posts when they have received a comment/answer.

Answer 1

[grant.hovhannisyan]

While there is no ideal cutoff for p-value (which has to be corrected for multiple testing) and fold change, you can have a look at a similar or reference studies and choose cutoffs based on them to be able to make fare comparisons with already published results.