Hi all, 

I am trying to run an analysis on 7 groups of chips (1 ctrl and 6 different conditions), each with 2 affymetrix chips.

I am trying to replicate what affylm gui would do but instead I thought of using a gcrma.mle correction.

After gathering as much info as I could from the forum ,still it seems to have stuck on how to choose which contrasts to use for the venn diagrams. (see part "#create vennDiagram" below). 

What I could consider important here is the ability to choose the contrasts that would be shown on the venn diagram , in a way that affylmGUI would enable the user to use.

Any help would really be appreciated.

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By the code used below I try to make a huge vennDiagram of all the 21 contrasts which is why possibly R returns"cannot allocate a vector of 340000 kb". Anyhow this would be a nice thing to have , possibly not usefull for the work I need to do ,  but just for the sake of seeing if this is possible to be done.
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# start by loading base libraries
library(affy)
library(limma)
library(gcrma)

#read in files

targets <- readTargets("RT_target.txt", row.names="Name")
ex1<-ReadAffy(filenames=targets$FileName)
ex1.gcrma.mle<-gcrma(ex1,estimate="mle",normalize=TRUE,summary.method = "medianpolish" )

#create lin model and contrasts
design <- model.matrix(~ -1+factor(c(1,1,2,2,3,3,4,4,5,5,6,6,7,7)))
colnames(design) <- c("CTRL", "IGF1", "ZOME","TGFb","CTED","INT6","ILTI")
fit <- lmFit(ex1.gcrma.mle, design)
contrast.matrix <- makeContrasts(IGF1-CTRL, ZOME-CTRL, TGFb-CTRL,CTED-CTRL,INT6-CTRL,ILTI-CTRL,ZOME - IGF1, TGFb-IGF1,CTED-IGF1,INT6-IGF1,ILTI-IGF1,TGFb-ZOME,CTED-ZOME,INT6-ZOME,ILTI-ZOME,CTED-TGFb,INT6-TGFb,ILTI-TGFb,INT6-CTED,ILTI-CTED,ILTI-INT6, levels=design)
fit2 <- contrasts.fit(fit, contrast.matrix)
fit2 <- eBayes(fit2)
topTable(fit2, coef=1, adjust="BH")

#create vennDiagram
results <- decideTests(fit2)
results
vennDiagram(results)



#Export toptable
library(affycoretools)
limma2annaffy(ex1,fit2,design,contrast.matrix, lib="hgu133a",adjust = "fdr",anncols = aaf.handler()[c(1:13)], number = 30, pfilt = NULL, fldfilt= NULL,tstat = TRUE, pval = TRUE, FC = TRUE,expression = TRUE, html = TRUE, text = FALSE, save = FALSE, addname =NULL, interactive = TRUE)


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