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Question: Filtering array data with nsFilter
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gravatar for emarram1
18 months ago by
emarram10
emarram10 wrote:

I am filtering the data that I am working with with nsFilter, 

filtered <- nsFilter(eset_rma, require.entrez = TRUE, remove.dupEntrez = TRUE, var.func = IQR ,var.cutoff = 0.5,var.filter = TRUE,filterByQuantile = FALSE, feature.exclude = "^AFFX")

 

when I use filterByQuantile = FALSE, instead of TRUE, what is this doing to my data?

after filtering I am using the limma package to decide which genes are different in each condition, and when I use filterByQuantile = FALSE I get more genes, why is that?

 

ADD COMMENTlink modified 18 months ago by Gordon Smyth32k • written 18 months ago by emarram10
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gravatar for Gordon Smyth
18 months ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

Please don't do this filtering. Using nsFilter() with var.filter=TRUE will sabotage any DE analysis you might do using limma. It would be better to take a simpler common-sense filtering approach, or even not to filter at all.

Have a look at previous posts on this topic, for example:

  Is filtering necessary to extract significant DE genes with limma ?

ADD COMMENTlink modified 18 months ago • written 18 months ago by Gordon Smyth32k
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