Hi Triantafyllos,
Triantafyllos Paparountas wrote:
> 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.
>
> ---------- 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. ----------
limma is not capable of creating Venn diagrams of greater than three
comparisons. Although it is possible to do higher order Venn diagrams,
I
don't think they would be easily programmed. See here for more
information:
http://en.wikipedia.org/wiki/Venn_diagram
>
>
> # 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)
This should just error out, saying that you cannot make a Venn diagram
with greater than three contrasts.
However, you should be able to make a Venn diagram with up to three
contrasts by simply subsetting your 'results' matrix. For instance
vennDiagram(results[,1:3])
HTH,
Jim
>
>
>
> #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)
>
>
> [[alternative HTML version deleted]]
>
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--
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623
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