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_Agile nt_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 [[alternative HTML version deleted]]

Dear Kart, See Section 11.8 of the limma User's Guide: http://bioconductor.org/packages/2.10/bioc/vignettes/limma/inst/doc /usersguide.pdf Best wishes Gordon --------------------------------------------- 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 http://www.wehi.edu.au http://www.statsci.org/smyth 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_Agi lent_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 > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}