[BioC] M values

[Sean Davis]

On Tue, Sep 30, 2008 at 10:47 AM, Jose Francisco Rodriguez
<francquimico at gmail.com> wrote:
> Hi:
> Thank You! I applied this command (MA$M) and obtained the values, but I'm
> having problems creating an excel table for those. I suppose that I should
> use write.table, but I dont know how to put the command without giving me an
> error.  Sorry but I'm still learning.

What have you tried?  And what error do you get?

Sean


> On 9/30/08, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>>
>> On Tue, Sep 30, 2008 at 9:42 AM, Jose Francisco Rodriguez
>> <francquimico at gmail.com> wrote:
>> > Hi:
>> > I performed a microarray (5 biological replicates) and analyzed using
>> > Limma.  The software gives me the M value as a combination from the 5
>> > biological replicates microarray.  In order to submit the data to GEO
>> > database we need the M-value for each array ( 5 M-values).  How can I do
>> > that? I'll appreciate your help.
>>
>> MA$M contains the M values for each array.
>>
>> Sean
>>
>> >  Below there is a copy of the sequence for the analysis:
>> >
>> > library(limma)
>> > library(geneplotter)
>> >
>> > ###Lee targets y image files
>> > targets=readTargets("maTargetFKS12.txt")
>> > RG=read.maimages(files=cbind(targets$FileNameCy3,targets$FileNameCy5),
>> >  source="imagene")
>> >
>> > ##lear gal
>> > gal=readGAL("013384_D_20050601.gal")
>> > gal=gal[1:nrow(RG$R),]
>> > ##asignar el gal
>> > RG$genes=gal
>> >
>> > ###definir los Spot Types y colores
>> > spottypes <- readSpotTypes() ##usamos el default que es SpotTypes
>> > RG$genes$Status <- controlStatus(spottypes, RG)
>> >
>> > ###definir el layour
>> > printer= list(ngrid.r=1,ngrid.c=1,nspot.r=107,nspot.c=101)
>> > RG$printer=structure(printer, class = "PrintLayout")
>> >
>> > ###normalize: background y normlize within
>> > RGoriginal = RG
>> > RG <- backgroundCorrect(RGoriginal, method="normexp", offset=50)
>> > MA = normalizeWithinArrays(RG,method="loess",bc.method="none")
>> >
>> > ##escoger los genes nadamas
>> > geneIndex = which(MA$genes$Status=="gene")
>> >
>> > ##preparar el disenyo para fit
>> > design = modelMatrix(targets,ref="WT")
>> >
>> > ###ver todos los MA plots como QC: todos OK!
>> > for(i in 1:6){
>>
>> > >  plotMA(MA[geneIndex,i],main=targets$Name[i],ylim=range(MA$M[geneIndex,]))
>> >  scan()
>> > }
>> >
>> > ###estimar los paramteros usando eBayes (moderated t-stat) y calcular
>> > FDR
>> > fit1 = lmFit(MA,design)
>> > fit1 = eBayes(fit1)
>> > tt=topTable(fit1,adjust="fdr",number=3000)
>> > tt=tt[tt$P.Value<=0.01,]
>> >
>> > ###Escoger genes para incluir en las graficas
>> > Index=as.numeric(rownames(tt))
>> > interestGenes <-
>> >
>> > c("CHS3","SLT2","PIR3","ECM4","ECM13","SPI1","ORF:YHR097C","MYO1","PIR3","HOG1","SWE1")
>> > interestIndex <- lapply(interestGenes,function(x)
>> > which(MA$genes$GeneName==x))
>> > names(interestIndex) <- interestGenes
>> >
>> > ##MA-PLOT
>> >
>> > plot(fit1$Amean[geneIndex],fit1$coef[geneIndex],pch=".",col="grey",ylab="M",xlab="A")
>> > points(fit1$Amean[Index],fit1$coef[Index],pch=16,col="blue",cex=.5)
>> > for(i in seq(along=interestGenes)){
>> >
>> >
>> > text(fit1$Amean[interestIndex[[i]]],fit1$coef[interestIndex[[i]]],interestGenes[i],cex=.5)
>> > }
>> >
>> > ##VOLCANO
>> >
>> > plot(fit1$coef[geneIndex],-log10(fit1$p.value[geneIndex]),pch=".",col="grey",xlab="M",ylab="-log_10
>> > p-value")
>> >
>> > points(fit1$coef[Index],-log10(fit1$p.value[Index]),pch=16,col="blue",cex=.5)
>> > for(i in seq(along=interestGenes)){
>> >
>> >
>> > text(fit1$coef[interestIndex[[i]]],-log10(fit1$p.value[interestIndex[[i]]]),interestGenes[i],cex=.5)
>> > }
>> >
>> >
>> > ###hacer xls file
>> > todos = topTable(fit1,adjust="fdr",number=10807)
>> > write.csv(todos,file="myo1.csv")
>> > --
>> > José F. Rodríguez Quiñones
>> > Graduate student
>> > School of Medicine
>> > Medical Sciences Campus
>> > University of Puerto Rico
>> >
>> >        [[alternative HTML version deleted]]
>> >
>> >
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>
>
>
> --
> José F. Rodríguez Quiñones
> Graduate student
> School of Medicine
> Medical Sciences Campus
> University of Puerto Rico