On 1/6/11 1:08 AM, Gordon K Smyth wrote:
Dear Kristen and Laurent,A possible (likely) explanation for the error is that your design matrix isn't of full column rank. Can you please check this:library(limma) is.fullrank(design)
Thanks. It was the case here.Future versions of estimateCRDisp() could test that and report an informative error message.
Best, Laurent
Best wishes Gordon On Mon, 3 Jan 2011, Laurent Gautier wrote:Hi Gordon,We seem to be experiencing the same issue here, although not originating from mglmOneGroup(), and edgeR-2.0.3 does not change the outcome:dge_disp <- estimateCRDisp(dge_list, design)Error in if (any(decr)) { : missing value where TRUE/FALSE neededtraceback()3: mglmLS(y, design, dispersion, offset = offset) 2: adjustedProfileLik(spline.disp[i], y.select, design = design, offset = offset.mat.select + lib.size.mat.select) 1: estimateCRDisp(dge_list, design)sessionInfo()R version 2.12.1 (2010-12-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] edgeR_2.0.3 loaded via a namespace (and not attached): [1] limma_3.6.9Best, Laurent On 1/3/11 4:36 AM, Gordon K Smyth wrote:Dear Kirsten, The error is arising in mglmOneGroup. I have just updated the relevant, code in edgeR version 2.0.3. Can you try it and see if you get the same error? With regard to the warning message, I can't think of any reason why edgeR would evaluate the Poisson density at a non-integer value if you have provided integer values. Have you checked that you have provided strictly integer counts? Try data$counts <- round(data$counts) data.cd = estimateCRDisp(data, design)to see if it makes any difference. If it does, then the data you enteredare not all integers. We are planning to revise estimateCRDisp() quite a bit during the next month or so. Best wishes GordonDate: Wed, 29 Dec 2010 15:39:01 -0500 From: <[email protected]> To: <[email protected]> Subject: [Bioc-sig-seq] error msg from edgeR estimateCRDisp Dear fellow edgeR users, I have an RNA-seq dataset with 2 factors and 24 samples (balanced) that I am attempting to analyze with edgeR. I keep encountering the following error when I use the estimateCRDisp function.data.cd = estimateCRDisp(data, design)Error in while (any(i)) { : missing value where TRUE/FALSE needed In addition: There were 50 or more warnings (use warnings() to see the first 50)warnings()Warning messages: 1: In dpois(y[i, ], lambda = mu[i, ], log = TRUE) : non-integer x = 530.381844 2: In dpois(y[i, ], lambda = mu[i, ], log = TRUE) : non-integer x = 676.500000 [etc]traceback()3: mglmOneGroup(y, offset, dispersion) 2: adjustedProfileLik(spline.disp[i], y.filt, design = design, offset = offset.mat.filt + lib.size.mat.filt) 1: estimateCRDisp(data, design)I see why the "dpois" function is giving an error, but I am not sure why a non-integer value is being sent to it. Any suggestions are greatly appreciated. Information about my session and commands follows: library(edgeR) targets = read.csv("design_file.csv") targets$factor_a = factor(targets$factor_a) targets$factor_b = factor(targets$factor_b) data = readDGE(targets) data = calcNormFactors(data) contrasts(targets$factor_a) = contr.sum(2) contrasts(targets$factor_b) = contr.sum(2) design = model.matrix(~factor_a+factor_b, data = targets) data.cd = estimateCRDisp(data, design)sessionInfo()R version 2.12.0 (2010-10-15) Platform: i386-pc-mingw32/i386 (32-bit) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] edgeR_2.0.2 loaded via a namespace (and not attached): [1] limma_3.6.9 tools_2.12.0 Kristen Dang, Ph.D. Computational Biologist Syngenta Biotechnology Research Triangle Park, NC______________________________________________________________________The information in this email is confidential and intend...{{dropped:4}}_______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing______________________________________________________________________ The information in this email is confidential and inte...{{dropped:7}}
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