This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Best cutoff for fold change of microarray data

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.

next-gen
• 4,433 views • link
written by Calangoa • 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.

• 0 views • link
written by Calangoa • Calangoa

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

• 0 views • link
written by GenoMax GenoMax

3 answers

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.

• 0 views • link
written by grant.hovhannisyan grant.hovhannisyan

• 0 views • link
written by Kevin Blighe Kevin Blighe

Thanks Kevin, I got it. in my data, I think FDR<0.05 and fold change >1.5 and <-1.5 for up- and dw-regulated genes respectively are the best (based on Mark R Dalman et al paper) but after normalization with R packages, we have log transformation of fold changes and I know if log FC is 2 it means 4 fold change for gene expression. and logFC -1= FC 0.5. it means, we don't have negative measure for fold change in statistic but have in biology. how shell i put it! what is the similar value of FC -1.5 for log FC? (?logFC=FC-1.5)

Thanks in advance

• 0 views • link
written by Calangoa • Calangoa

Fold change can not be negative, but log-transformed fold change can. Imagine your initial expression is 100 and after a treatment it decreased to 50. The fold change is 0.5, and log(2) fold change is -1.

• 0 views • link
written by grant.hovhannisyan grant.hovhannisyan

in my data, I think FDR<0.05 and fold change >1.5 and <-1.5 for up- and dw-regulated genes respectively are the best (based on Mark R Dalman et al paper) but after normalization with R packages, we have log transformation of fold changes and I know if log FC is 2 it means 4 fold change for gene expression. and logFC -1= FC 0.5. it means, we don't have negative measure for fold change in statistic but have in biology. how shell i put it! what is the similar value of FC -1.5 for log FC? (?logFC=FC-1.5)

Thanks in advance

• 0 views • link
written by Calangoa • Calangoa

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

This comment belongs under Kevin's answer. If you can post it there I will delete it from this spot.

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this