Hi all, I am trying to understand what is the best practice when preprocessing microarray data using a detection filter (on scanner p-value). Suppose I have a microarray dataset that I have to normalize with Loess and correct with ComBat. In which order have I to apply detection filter with regards to the other operations?
In my experimental design I have two pipelines to test:
Normalize per sample between 0 - 1
ComBat
Loess normalization between samples
and
Loess normalization between samples
ComBat
Is there any best practice to apply when dealing with detection filter? Where have I to apply detection filtering?
Thanks
•
written
by
fbrundu
1 answer
Consider filtering on per-feature variance rather than detection p-value. I would apply a filter immediately prior to differential expression analysis. That said, I do not know that there is a "best practice" for all datasets and platforms.
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