Entering edit mode
Dear Huajing Teng,
See
https://www.stat.math.ethz.ch/pipermail/bioconductor/2012-November/049
087.html
for a solution. The problem is arising because you have different
numbers
of patients in the two groups (5 males but 4 female). This causes one
of
the columns of your design matrix to be all zero. You will need to
remove
the all zero column.
Best wishes
Gordon
> Date: Tue, 8 Jan 2013 16:39:22 -0800 (PST)
> From: "Huajing Teng [guest]" <guest at="" bioconductor.org="">
> To: bioconductor at r-project.org, tenghj at mail.biols.ac.cn
> Subject: [BioC] detailed analysis process of \"Comparisons Both
> Between and Within Subjects\" of edgeR
>
>
> Dear Dr.Smyth,
> I am very interested in "Comparisons Both Between and Within
Subjects"
> of edgeR. Because one of my study is according to this design. But i
> found some detailed analysis have not been provided in the manual
(After
> estimating the dispersions (code not shown), we can fit a linear
> model:), and i met some difficulty in using this pipline. When i
used y
> <- estimateGLMCommonDisp(y, design, verbose=TRUE), I got an error:
error
> in solve.default(R, t(beta)) : Lapack routine dgesv: system is
exactly
> singular
>
> I wonder whether you can provide some detailed analysis process
> (especially in data reading, dispersion evaluation ). Thanks for
your
> kind assistance.
>
> -- output of sessionInfo():
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("edgeR") biocLite("limma")
> library(edgeR)
>> targets <- read.delim("F:/teng/thyroidcarcinoma/gene_exp.diff/edgeR
/2nd/geneexpression/allnosui/design.txt", check.names=FALSE,
stringsAsFactors=FALSE)
>> targets
>> Patient <- gl(5,2,length=18)
>> Sex <- factor(targets$Sex, levels=c("M","F"))
>> Treatment <- factor(targets$Treatment, levels=c("N","T"))
>> data.frame(Sex,Patient,Treatment)
>> y <- read.delim("F:/teng/thyroidcarcinoma/gene_exp.diff/edgeR/2nd/g
eneexpression/allnosui/genecount.txt", row.names=1, header=T,
stringsAsFactors=FALSE)
>> design <- model.matrix(~Sex+Sex:Patient+Sex:Treatment)
>> rownames(design) <- colnames(y)
>> y <- estimateGLMCommonDisp(y, design, verbose=TRUE)
> #error:
> #error in solve.default(R, t(beta)) : Lapack routine dgesv: system
is exactly singular
>
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