Thanks, Mark; yes, in works in R 2.14 : it did not work in Rstudio and in R 2.12. On Fri, Nov 18, 2011 at 12:39 PM, Mark Robinson <mark.robinson@imls.uzh.ch>wrote: > > > On 18.11.2011, at 21:27, Bogdan Tanasa wrote: > > > Dear all, > > > > are the functions "estimateGLMCommonDisp" and "estimateGLMTagwiseDisp" > > available in edgeR on any platform ? I am using it on Linux/Ubuntu and > > apparently, these functiosn are not available. > > > What version of R/edgeR are you using? Perhaps you have an old version? > These functions have been around for awhile. What does sessionInfo() give? > > Mark > > > > > > > thanks, > > > > Bogdan > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]

Hi Mark, I have two samples "Y" and "S" (with no replicates), and following edgeR manual on "what to do if you do not have replicates", I am getting the following results below. The end message is "No residual df: cannot estimate dispersion". Please could you let me know what is going wrong .. Thanks a lot ! >raw.data <- read.delim("file") >d <- raw.data[,2:3] >rownames(d) <- raw.data[,1] > group <- factor(c("Y","S")) > design <- model.matrix(~group) >d <- DGEList(counts = d, group=group) Calculating library sizes from column totals. > dim(d) [1] 4013 2 > d <- calcNormFactors(d) > d An object of class "DGEList" $samples group lib.size norm.factors Y Y 628062 1.049011 S S 422542 0.953279 $counts Y S chr8:53670099-53691880 132 109 chr8:71033673-71122126 221 107 chr8:74069636-74074658 7 1 chr6:72172478-72187779 203 114 chr6:72096548-72115900 36 15 4008 more rows ... $all.zeros chr8:53670099-53691880 chr8:71033673-71122126 chr8:74069636-74074658 FALSE FALSE FALSE chr6:72172478-72187779 chr6:72096548-72115900 FALSE FALSE 4008 more elements ... > d<-estimateGLMCommonDisp(d,design,method="deviance",robust="TRUE",subs et=NULL) Warning message: In estimateGLMCommonDisp.default(y = y$counts, design = design, : No residual df: cannot estimate dispersion For Common Dispersion (no GLM modeling): > d<-estimateCommonDisp(d,design) Warning message: In estimateCommonDisp(d, design) : There is no replication. Setting common dispersion to 0. > d An object of class "DGEList" $samples group lib.size norm.factors Y Y 628062 1.049011 S S 422542 0.953279 $counts Y S chr8:53670099-53691880 132 109 chr8:71033673-71122126 221 107 chr8:74069636-74074658 7 1 chr6:72172478-72187779 203 114 chr6:72096548-72115900 36 15 4008 more rows ... $all.zeros chr8:53670099-53691880 chr8:71033673-71122126 chr8:74069636-74074658 FALSE FALSE FALSE chr6:72172478-72187779 chr6:72096548-72115900 FALSE FALSE 4008 more elements ... $common.dispersion [1] 1e-16 $pseudo.alt Y S chr8:53670099-53691880 103.192083 139.42506 chr8:71033673-71122126 172.781586 136.86720 chr8:74069636-74074658 5.453794 1.30187 chr6:72172478-72187779 158.707305 145.81970 chr6:72096548-72115900 28.129216 19.20588 4008 more rows ... $conc $conc.common chr8:53670099-53691880 chr8:71033673-71122126 chr8:74069636-74074658 2.270073e-04 3.089534e-04 7.535477e-06 chr6:72172478-72187779 chr6:72096548-72115900 2.985930e-04 4.803864e-05 4008 more elements ... $conc.group S Y chr8:53670099-53691880 2.706055e-04 2.003510e-04 chr8:71033673-71122126 2.656403e-04 3.354361e-04 chr8:74069636-74074658 2.482619e-06 1.062467e-05 chr6:72172478-72187779 2.830186e-04 3.081155e-04 chr6:72096548-72115900 3.723929e-05 5.464117e-05 4008 more rows ... $common.lib.size $pseudo Y S chr8:53670099-53691880 103.192083 139.42506 chr8:71033673-71122126 172.781586 136.86720 chr8:74069636-74074658 5.453794 1.30187 chr6:72172478-72187779 158.707305 145.81970 chr6:72096548-72115900 28.129216 19.20588 4008 more rows ... $conc $conc.common chr8:53670099-53691880 chr8:71033673-71122126 chr8:74069636-74074658 2.270073e-04 3.089534e-04 7.535477e-06 chr6:72172478-72187779 chr6:72096548-72115900 2.985930e-04 4.803864e-05 4008 more elements ... $conc.group S Y chr8:53670099-53691880 2.706055e-04 2.003510e-04 chr8:71033673-71122126 2.656403e-04 3.354361e-04 chr8:74069636-74074658 2.482619e-06 1.062467e-05 chr6:72172478-72187779 2.830186e-04 3.081155e-04 chr6:72096548-72115900 3.723929e-05 5.464117e-05 4008 more rows ... $N [1] 515153 On Fri, Nov 18, 2011 at 12:39 PM, Mark Robinson <mark.robinson@imls.uzh.ch>wrote: > > > On 18.11.2011, at 21:27, Bogdan Tanasa wrote: > > > Dear all, > > > > are the functions "estimateGLMCommonDisp" and "estimateGLMTagwiseDisp" > > available in edgeR on any platform ? I am using it on Linux/Ubuntu and > > apparently, these functiosn are not available. > > > What version of R/edgeR are you using? Perhaps you have an old version? > These functions have been around for awhile. What does sessionInfo() give? > > Mark > > > > > > > thanks, > > > > Bogdan > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]