Question

Problem in analyzing microarray with duplicate or triplicate data

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peirinl • 0

@peirinl-14078

Last seen 4.6 years ago

I want to use open TG-gates and drugmatrix data to do toxicogenomics analysis. Within the data, there is duplicate or triplicate data for each different dose of different chemicals. I arranged the data as this

               Chem_Name     Class       File_name
         1.    Chem A        toxic       ChemA_01.CEL
         2.    Chem A        toxic       ChemA_02.CEL
         3.    Chem A        toxic       ChemA_03.CEL
         4.    Chem B        toxic       ChemB_01.CEL
         5.    Chem B        toxic       ChemB_02.CEL
          .......
         31.   Chem G       non-toxic    ChemG_01.CEL
         32.   Chem G       non-toxic    ChemG_02.CEL
         33.   Chem G       non-toxic    ChemG_03.CEL   
         35.   Chem H       non-toxic    ChemH_01.CEL
         36.   Chem H       non-toxic    ChemH_02.CEL

May I know 1. How to run arrayQualityMetrics?

  arrayQualityMetrics(expressionset = raw_data, outdir = tempdir(), force = TRUE, 
  do.logtransform = TRUE, intgroup = c(   which factor to use????,    which factor to use???))

2. How to set the model.matrix for Limma? I would like to extract the differentially expressed genes after exposed to toxic chemicals.

microarray limma • 839 views

ADD COMMENT • link 4.6 years ago peirinl • 0

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It's hard to provide help with the model matrix without knowing what you are trying to test ... I can take a guess, but that doesn't really help anybody: can be you be a bit more explicit?

Also, this looks to will be a pretty straightforward analysis and likely is covered by the many examples outlines in the limma user guide, have you read that yet?

ADD REPLY • link 4.6 years ago Steve Lianoglou ★ 13k