Dear All,
I have analyzed a dataset for differential gene expression using LIMMA. The requirement was to select probesets with highest value of expression. I notice that there is a change in results for when i filter for probesets before and after performing LIMMA. The logFC  and gene list remains the same, only change is in the p-value and B Value, again this is possible because the probesets are not averaged to the gene level but retained on maximum expression there by not having any affect of the filtering on the fold change.

I can see that a similar question had been asked before https://stat.ethz.ch/pipermail/bioconductor/2011-June/039936.html

Would be grateful if someone can please tell me if its best to filter before any statistical analysis or after? I am leaning towards 'filter before always' but though will gather more views on the same.

Many Thanks.

Regards,
Ekta
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