Re: [R]  microarray analysis: contrast matrix problem

[Martin Morgan]

Hi Oihane

lmFit is from the limma package, and the limma package is part of the 
Bioconductor project; the Bioconductor mailing list

   http://bioconductor.org/help/mailing-list/

(follow the 'Post' link) may be a more appropriate place to post this question 
(after searching the archive) if there is no answer here.

Martin

On 05/21/2013 04:49 AM, Oihane Irazoki wrote:
> Hi! I'm sorry for bothering you. I'm a new R-user and I'm having some problems while doing a microarray analysis. I'm comparing the whole genome array of a Salmonella serovar to another 25, and my goal is to determine which genes are differentially expressed. I'm using limma package and running the next code,
>
>
> DIFFERENTIAL EXPRESSION i
> #several groups comparisson (by serovars)
>
> groups <- read.table("ClusteringSamples.txt", head=T, sep='\t')
>
> f <- factor(groups$Serovar)
> design <- model.matrix(~0 + f)
>
> colnames(design) <- c("Abortusovis", "Agona", "Anatum", "Arizonae", "Braenderup",
>         "Bredeney", "Cholerasuis", "Derby", "Enteritidis", "Gallinarum", "Goelzau",
>          "Hadar", "Havana", "Infantis", "Kedougou", "Mbandaka", "Mikawasima", "Ohio",
>          "ParatiphyA", "ParatiphyB", "Pos.Control", "Pullorum", "Typhi",
>          "Typhimurium", "Virchow")
>             #Convertir a vectores!
>
> summary(is.na(data)) #check if there is any missing value in the dataset.
>
> fit <- lmFit(data, design)
>
> contrast.matrix <- makeContrasts(Abortusovis-Pos.Control, Agona-Pos.Control,
>          Anatum-Pos.Control, Arizonae-Pos.Control, Braenderup-Pos.Control,
>          Bredeney-Pos.Control, Cholerasuis-Pos.Control, Derby-Pos.Control,
>          Enteritidis-Pos.Control, Gallinarum-Pos.Control, Goelzau-Pos.Control,
>          Hadar-Pos.Control, Havana-Pos.Control, Infantis-Pos.Control,
>          Kedougou-Pos.Control, Mbandaka-Pos.Control, Mikawasima-Pos.Control,
>          Ohio-Pos.Control, ParatiphyA-Pos.Control, ParatiphyB-Pos.Control,
>          Pos.Control-Pos.Control, Pullorum-Pos.Control, Typhi-Pos.Control,
>          Typhimurium-Pos.Control, Virchow-Pos.Control,
>                                 levels=design)
>
> fit1 <- contrasts.fit(fit, contrast.matrix)
> fit2 <- eBayes(fit1)
>
> But when I try to run eBayes correction to then compute topTable and get those differentially expressed genes, I get and error back:
>
>
> Error in eigen(cor.matrix, symmetric = TRUE) :
>    infinite or missing values in 'x'
> In addition: Warning messages:
> 1: In ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim,  :
>    Estimation of var.prior failed - set to default value
> 2: In cov2cor(object$cov.coefficients) :
>    diag(.) had 0 or NA entries; non-finite result is doubtful
>
> I try to eliminate those missing values, but then I only can compute the contrast matrix of 13 of my 25 different serovars.
> How can I solve the problem? I'll appreciate the all the help and advices.
>
> Oihane
> __
> Oihane Irazoki Sanchez
> PhD Student, Molecular Microbiology
>
> Depart. de Genètica i Microbiologia (Facultat de Biociències)
> UAB, 08193 Bellaterra (Barcelona), Spain
>
> Phone: 34-660938553
> E-mail: oihane.irazoki at uab.cat / o.irazoki at gmail.com
>
>
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>
>
>
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