[BioC] Pre-filtering before differential expression analysis in LIMMA

Gordon K Smyth smyth at wehi.EDU.AU
Tue Mar 13 23:49:32 CET 2012

Dear Kart,

See Section 11.8 of the limma User's Guide:


Best wishes

Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
smyth at wehi.edu.au

On Tue, 13 Mar 2012, Karthik K N wrote:

> Dear Members,
> Is there any way to pre-filter the dataset in LIMMA before going on to
> differential expression analysis?
> I am using Agilent microarrays and would really like to filter out
> genes/spots based on flags. Is this possible in LIMMA? Or is there any
> better way to filter than using flags in LIMMA?
> My dataset has a lot of genes and I really think I should use stringent
> filtering before going onto analysis part. I am thinking of using kind of
> code given in
> http://matticklab.com/index.php?title=Single_channel_analysis_of_Agilent_microarray_data_with_Limma
> (Thanks
> to John Mattick <http://matticklab.com/index.php?title=John_Mattick> and Gordon
> Smyth).
> I would also be extremely grateful if someone could share a bit of such
> codes since I am just a newbie.
> Thanks a lot in advance for your help.
> Kart

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