[BioC] 2 color microarray and decidetests output

[James W. MacDonald]

Hi Srinivas,

On 1/24/2012 4:31 AM, Srinivas M. Srikanth wrote:
> Hi all,
>
> I am working with two color microrray data and have three different stages
> of cancer along with normal, all normalized with a universal Normal. I
> analyzed the data using Limma package in R.My workflow is as below:
>
> library(limma)
> targets<-readTargets(filename)
> RG<-read.maimages(targets,
> source="genepix")
> RG$genes<-readGAL()
> MA<-normalizeWithinArrays(RG,method="loess")
> plotMA(RG)
> plotMA(MA)
> MA<-normalizeBetweenArrays(MA,method="aquantile")
> design=modelMatrix(MA,ref="Control")
> fit<-lmfit(MA,design)
> fit2<-ebayes(fit)
> contrastmatrix<-makeContrasts("StageI-Normal","StageII-Normal","StageIII-Normal","StageIII-StageI","StageII-StageI","StageIII-StageII",levels=design)
> fit3<-contrasts.fit(fit2,contrastsmatrix)
> fit3<-ebayes(fi3)
> results<- decideTests(fit3,method="global")
> vennDiagram(results[,1:3])
>
> I want to print the common genes which are common in all three stages and
> also find common signature set of genes among different stages, please help
> on how I should proceed further.

There is a function vennSelect() in my affycoretools package that is 
designed to print out all the genes in each section of a Venn diagram. 
It is intended to annotate as well, so if you don't have an annotation 
package for your chip you will either need to make one, or you could 
debug() vennSelect() and grab the results before it gets to the point 
where it tries to annotate.

I am not sure exactly what you mean by 'common signature set of genes'. 
Perhaps you should look at e.g., GSEABase, GOstats, Category, etc. All 
these packages have vignettes that you could read.

Best,

Jim


>
>
> The target file is as below:
> SampleNumber    FileName    Cy3    Cy5
> 1    CN 310_N.gpr    Control    Normal
> 2    CN 314_N.gpr    Control    Normal
> 3    CN 318_N.gpr    Control    Normal
> 4    CN 321_N.gpr    Control    Normal
> 5    CN 322_N.gpr    Control    Normal
> 6    CT 1015_II.gpr    Control    StageII
> 7    CT1021_II.gpr    Control    StageII
> 8    CT 1063_II.gpr    Control    StageII
> 9    CT1077_II.gpr    Control    StageII
> 10    CT1099_III.gpr    Control    StageIII
> 11    CT 1131_III.gpr    Control    StageIII
> 12    CT 1138_I.gpr    Control    StageI
> 13    CT 1178_III.gpr    Control    StageIII
> 14    CT 1179_III.gpr    Control    StageIII
> 15    CT 1187_III.gpr    Control    StageIII
> 16    CT500_I.gpr    Control    StageI
> 17    CT503_II.gpr    Control    StageII
> 18    CT 510_I.gpr    Control    StageI
> 19    CT 513_I.gpr    Control    StageI
> 20    CT 514_I.gpr    Control    StageI
> 21    CT 515_I.gpr    Control    StageI
> 22    CT 800_II.gpr    Control    StageII
> 23    CT 805_II.gpr    Control    StageII
> 24    CT 809_III.gpr    Control    StageIII
> 25    CT 833_I.gpr    Control    StageI
> 26    CT 843_I.gpr    Control    StageI
> 27    CT 859_III.gpr    Control    StageIII
> 28    CT 871_II.gpr    Control    StageII
> 29    CT 905_III.gpr    Control    StageIII
> 30    CT 935_II.gpr    Control    StageII
>
>
> Regards,
> Srikanth
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

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