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Question: regarding edgeR
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gravatar for deepika lakhwani
5.8 years ago by
deepika lakhwani170 wrote:
hello.... i am trying ti find out differential gene by the edgeR package.i have 2 transcriptome libraries, one is control and other is experimental. when i estimate overall dispersion for the dataset. its gives me warning message: Warning message: In estimateGLMCommonDisp.default(y = y$counts, design = design, : No residual df: setting dispersion to NA and without dispersion value, i can not find DE genes.now what i do?please anyone tell me. these are the commands: rawdata1 <- read.delim("banana.txt", check.names=FALSE, stringsAsFactors=FALSE) > head(rawdata) 0day ethy 1 contig00001 625 115 2 contig00002 662 88 3 contig00003 466 563 4 contig00004 610 98 5 contig00005 72 21 6 contig00006 82 2 > library(edgeR) > y <- DGEList(counts=rawdata[,2:3], genes=rawdata[,1:1]) Calculating library sizes from column totals. > y <- calcNormFactors(y) > y$samples group lib.size norm.factors 0day 1 34450 1.1292933 ethy 1 25198 0.8855096 > plotMDS(y) Error in cmdscale(as.dist(dd), k = ndim) : 'k' must be in {1, 2, .. n - 1} > Patient <- factor(c(0,1)) > Tissue <- factor(c("N","T")) > data.frame(Sample=colnames(y),Patient,Tissue) Sample Patient Tissue 1 0day 0 N 2 ethy 1 T > design <- model.matrix(~Patient+Tissue) > rownames(design) <- colnames(y) > y <- estimateGLMCommonDisp(y, design, verbose=TRUE) Warning message: In estimateGLMCommonDisp.default(y = y$counts, design = design, : No residual df: setting dispersion to NA > y <- estimateGLMCommonDisp(y) > y <- estimateGLMTrendedDisp(y) > y <- estimateGLMTagwiseDisp(y) Warning message: In movingAverageByCol(apl[o, ], width = 1000) : reducing moving average width to nrow(x) > fit <- glmFit(y, design) Error in beta[i, ] <- z %*% X : number of items to replace is not a multiple of replacement length > rawdata1 <- read.delim("banana.txt", check.names=FALSE, stringsAsFactors=FALSE) > library(edgeR) > y <- DGEList(counts=rawdata[,2:3], genes=rawdata[,1:1]) Calculating library sizes from column totals. > y <- calcNormFactors(y) > y$samples group lib.size norm.factors 0day 1 34450 1.1292933 ethy 1 25198 0.8855096 > plotMDS(y) Error in cmdscale(as.dist(dd), k = ndim) : 'k' must be in {1, 2, .. n - 1} please help me. regards deepika [[alternative HTML version deleted]]
ADD COMMENTlink modified 5.8 years ago by Steve Lianoglou12k • written 5.8 years ago by deepika lakhwani170
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gravatar for Steve Lianoglou
5.8 years ago by
Denali
Steve Lianoglou12k wrote:
Hi, On Wednesday, August 29, 2012, deepika lakhwani wrote: > hello.... > > i am trying ti find out differential gene by the edgeR package.i have 2 > transcriptome libraries, one is control and other is experimental. There is a section in the edgeR user guide that deals with the scenario where you do not have any replicates (which is the situation you seem to be in) Follow the instructions there. HTH -steve > when i estimate overall dispersion for the dataset. its gives me warning > message: > > Warning message: > In estimateGLMCommonDisp.default(y = y$counts, design = design, : > No residual df: setting dispersion to NA > > and without dispersion value, i can not find DE genes.now what i do?please > anyone tell me. > > these are the commands: > > rawdata1 <- read.delim("banana.txt", check.names=FALSE, > stringsAsFactors=FALSE) > > head(rawdata) > 0day ethy > 1 contig00001 625 115 > 2 contig00002 662 88 > 3 contig00003 466 563 > 4 contig00004 610 98 > 5 contig00005 72 21 > 6 contig00006 82 2 > > library(edgeR) > > y <- DGEList(counts=rawdata[,2:3], genes=rawdata[,1:1]) > Calculating library sizes from column totals. > > y <- calcNormFactors(y) > > y$samples > group lib.size norm.factors > 0day 1 34450 1.1292933 > ethy 1 25198 0.8855096 > > plotMDS(y) > Error in cmdscale(as.dist(dd), k = ndim) : > 'k' must be in {1, 2, .. n - 1} > > Patient <- factor(c(0,1)) > > Tissue <- factor(c("N","T")) > > data.frame(Sample=colnames(y),Patient,Tissue) > Sample Patient Tissue > 1 0day 0 N > 2 ethy 1 T > > design <- model.matrix(~Patient+Tissue) > > rownames(design) <- colnames(y) > > y <- estimateGLMCommonDisp(y, design, verbose=TRUE) > Warning message: > In estimateGLMCommonDisp.default(y = y$counts, design = design, : > No residual df: setting dispersion to NA > > y <- estimateGLMCommonDisp(y) > > y <- estimateGLMTrendedDisp(y) > > y <- estimateGLMTagwiseDisp(y) > Warning message: > In movingAverageByCol(apl[o, ], width = 1000) : > reducing moving average width to nrow(x) > > fit <- glmFit(y, design) > Error in beta[i, ] <- z %*% X : > number of items to replace is not a multiple of replacement length > > rawdata1 <- read.delim("banana.txt", check.names=FALSE, > stringsAsFactors=FALSE) > > library(edgeR) > > y <- DGEList(counts=rawdata[,2:3], genes=rawdata[,1:1]) > Calculating library sizes from column totals. > > y <- calcNormFactors(y) > > y$samples > group lib.size norm.factors > 0day 1 34450 1.1292933 > ethy 1 25198 0.8855096 > > plotMDS(y) > Error in cmdscale(as.dist(dd), k = ndim) : > 'k' must be in {1, 2, .. n - 1} > > > > please help me. > > regards > deepika > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <javascript:;> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact [[alternative HTML version deleted]]
ADD COMMENTlink written 5.8 years ago by Steve Lianoglou12k
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