Question: At Which Step Apply A Detection Filter When Preprocessing Microarray Data? (Before/After Normalization, Batch Effects Removal)
0
gravatar for fbrundu
5.7 years ago by
fbrundu280
European Union
fbrundu280 wrote:

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

ADD COMMENTlink modified 5.7 years ago by Sean Davis25k • written 5.7 years ago by fbrundu280
1
gravatar for Sean Davis
5.7 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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.

ADD COMMENTlink written 5.7 years ago by Sean Davis25k
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