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/ge neexpression/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 -- Sent via the guest posting facility at bioconductor.org.

Could you share what your "targets On Tue 08 Jan 2013 04:39:22 PM PST, Huajing Teng [guest] wrote: > > 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 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hello, (Sorry about the incomplete message before. I tripped and fell on the send button.) I think you might need to share what your targets file and your design matrix look like. If I had to guess, I would guess that your design matrix has too many columns for some reason (specifically, more columns than degrees of freedom). If you show us your design matrix, we could verify whether this is indeed the case, or whether there is some other problem. -Ryan Thompson On 01/08/2013 04:39 PM, Huajing Teng [guest] wrote: > 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 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor