Hi guys

I have a dataset with 100 sample and 54000 probID,I used to think that if I filter those of probID with little variation, I can reduce the number of features and then in multiple testing with limma in would give me fewer errors and finally fewer noises, but now I found that if I use genefilter package, it changes the distribution of variance and it will interfere with limma package

let me know if I am mistaken and tell me if there are other option except genefiltering package

tnx

Pretty much anything except for variance filtering works fine, and there have been quite a few posts on this, for example here is one from a week or so ago:

  Suggestions for non-specific filtering criteria with limma

With microarrays you could simply filter out probes with low average log-expression (fit$Amean in a limma fit object), or there are ways to use control probes to make a more objective judgement if your arrays have them.