I have a question about the edgeR package in R. I have a dataframe and design matrix like below and every time i get the same error. Can anyone help me with the follow code and error? >data.frame WT_SHAM1 WT_SHAM2 WT_SHAM3 WT_SHAM4 WT_SHAM5 WT_SHAM6 WT_CSD1 WT_CSD2 WT_CSD3 WT_CSD4 WT_CSD5 WT_CSD6 RQ_SHAM1 RQ_SHAM2 RQ_SHAM3 RQ_SHAM4 RQ_SHAM5 RQ_SHAM6 RQ_CSD1 RQ_CSD2 RQ_CSD3 RQ_CSD4 ENSMUSG00000002012 553 1167 660 1736 365 760 971 961 974 1790 1458 2843 556 871 1263 1142 1043 1919 969 794 771 682 ENSMUSG00000028182 2 11 3 8 2 8 1 10 3 39 5 19 1 5 34 13 1 3 8 13 5 1 ENSMUSG00000002017 26 50 50 42 100 140 29 31 41 69 147 99 20 43 74 135 63 92 55 44 23 68 ENSMUSG00000028184 381 664 442 762 476 653 618 376 353 806 1271 1938 381 306 859 687 249 1596 773 635 240 562 ENSMUSG00000002015 399 956 531 1725 1217 1111 668 928 350 549 828 2199 480 702 1611 1448 331 678 1199 1014 652 913 >design (Intercept) strain CSD 1 1 0 0 2 1 0 0 3 1 0 0 4 1 0 0 5 1 0 0 6 1 0 0 7 1 0 1 8 1 0 1 9 1 0 1 10 1 0 1 11 1 0 1 12 1 0 1 13 1 1 0 14 1 1 0 15 1 1 0 16 1 1 0 17 1 1 0 18 1 1 0 19 1 1 1 20 1 1 1 21 1 1 1 22 1 1 1 >d <- DGEList(data_files, lib.size=colSums(data_files)) An object of class "DGEList" $samples group lib.size norm.factors WT_SHAM1 1 6154923 1 WT_SHAM2 1 12269537 1 WT_SHAM3 1 8785094 1 WT_SHAM4 1 19878567 1 WT_SHAM5 1 13420516 1 17 more rows ... $counts WT_SHAM1 WT_SHAM2 WT_SHAM3 WT_SHAM4 WT_SHAM5 WT_SHAM6 WT_CSD1 WT_CSD2 WT_CSD3 WT_CSD4 WT_CSD5 WT_CSD6 RQ_SHAM1 RQ_SHAM2 RQ_SHAM3 RQ_SHAM4 RQ_SHAM5 RQ_SHAM6 RQ_CSD1 RQ_CSD2 RQ_CSD3 RQ_CSD4 ENSMUSG00000002012 553 1167 660 1736 365 760 971 961 974 1790 1458 2843 556 871 1263 1142 1043 1919 969 794 771 682 ENSMUSG00000028182 2 11 3 8 2 8 1 10 3 39 5 19 1 5 34 13 1 3 8 13 5 1 ENSMUSG00000002017 26 50 50 42 100 140 29 31 41 69 147 99 20 43 74 135 63 92 55 44 23 68 ENSMUSG00000028184 381 664 442 762 476 653 618 376 353 806 1271 1938 381 306 859 687 249 1596 773 635 240 562 ENSMUSG00000002015 399 956 531 1725 1217 1111 668 928 350 549 828 2199 480 702 1611 1448 331 678 1199 1014 652 913 23841 more rows ... $all.zeros ENSMUSG00000002012 ENSMUSG00000028182 ENSMUSG00000002017 ENSMUSG00000028184 ENSMUSG00000002015 FALSE FALSE FALSE FALSE FALSE 23841 more elements ... >d <- calcNormFactors(d) An object of class "DGEList" $samples group lib.size norm.factors WT_SHAM1 1 6154923 0.9765708 WT_SHAM2 1 12269537 0.9914651 WT_SHAM3 1 8785094 0.9693995 WT_SHAM4 1 19878567 0.9193010 WT_SHAM5 1 13420516 1.0142604 17 more rows ... $counts WT_SHAM1 WT_SHAM2 WT_SHAM3 WT_SHAM4 WT_SHAM5 WT_SHAM6 WT_CSD1 WT_CSD2 WT_CSD3 WT_CSD4 WT_CSD5 WT_CSD6 RQ_SHAM1 RQ_SHAM2 RQ_SHAM3 RQ_SHAM4 RQ_SHAM5 RQ_SHAM6 RQ_CSD1 RQ_CSD2 RQ_CSD3 RQ_CSD4 ENSMUSG00000002012 553 1167 660 1736 365 760 971 961 974 1790 1458 2843 556 871 1263 1142 1043 1919 969 794 771 682 ENSMUSG00000028182 2 11 3 8 2 8 1 10 3 39 5 19 1 5 34 13 1 3 8 13 5 1 ENSMUSG00000002017 26 50 50 42 100 140 29 31 41 69 147 99 20 43 74 135 63 92 55 44 23 68 ENSMUSG00000028184 381 664 442 762 476 653 618 376 353 806 1271 1938 381 306 859 687 249 1596 773 635 240 562 ENSMUSG00000002015 399 956 531 1725 1217 1111 668 928 350 549 828 2199 480 702 1611 1448 331 678 1199 1014 652 913 23841 more rows ... $all.zeros ENSMUSG00000002012 ENSMUSG00000028182 ENSMUSG00000002017 ENSMUSG00000028184 ENSMUSG00000002015 FALSE FALSE FALSE FALSE FALSE 23841 more elements ... >d <- estimateGLMCommonDisp(d, design=design) $common.dispersion [1] 0.2005023 > d <- estimateGLMTrendedDisp(d, design=design) Error in cutWithMinN(abundance[!all.zero], intervals = nbins, min.n = min.n) : function has failed, perhaps because of too many tied values? -- output of sessionInfo(): > sessionInfo() R version 2.14.2 (2012-02-29) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252 LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C [5] LC_TIME=Dutch_Netherlands.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] edgeR_2.4.6 limma_3.10.3 -- Sent via the guest posting facility at bioconductor.org.

Dear Lisannne, Please have a closer look at the posting guide http://www.bioconductor.org/help/mailing-list/posting-guide/ which advises you to "Ensure that you are using the latest Bioconductor release and that your installed packages are up-to-date." You are using software that is two Bioconductor releases out of date, and it isn't worth anyone's time to answer questions about software that is no longer current. There's a very good chance that simply installing the current software would make your problem go away. The posting guide also asks you to identify yourself, which usually means to give your full name and institution. I know that lots of posters on this mailing list don't do that, but I certainly feel better spending time on a real person and fellow professional rather than on an hotmail account. Best wishes Gordon --------------------------------------------- Professor Gordon K Smyth, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Vic 3052, Australia. http://www.statsci.org/smyth > Date: Fri, 2 Nov 2012 01:26:30 -0700 (PDT) > From: "Lisanne [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, lisannevijfhuizen at hotmail.com > Subject: [BioC] R EdgeR package error > > I have a question about the edgeR package in R. I have a dataframe and > design matrix like below and every time i get the same error. Can anyone > help me with the follow code and error? > >data.frame > WT_SHAM1 WT_SHAM2 WT_SHAM3 WT_SHAM4 WT_SHAM5 WT_SHAM6 WT_CSD1 WT_CSD2 WT_CSD3 WT_CSD4 WT_CSD5 WT_CSD6 RQ_SHAM1 RQ_SHAM2 RQ_SHAM3 RQ_SHAM4 RQ_SHAM5 RQ_SHAM6 RQ_CSD1 RQ_CSD2 RQ_CSD3 RQ_CSD4 > ENSMUSG00000002012 553 1167 660 1736 365 760 971 961 974 1790 1458 2843 556 871 1263 1142 1043 1919 969 794 771 682 > ENSMUSG00000028182 2 11 3 8 2 8 1 10 3 39 5 19 1 5 34 13 1 3 8 13 5 1 > ENSMUSG00000002017 26 50 50 42 100 140 29 31 41 69 147 99 20 43 74 135 63 92 55 44 23 68 > ENSMUSG00000028184 381 664 442 762 476 653 618 376 353 806 1271 1938 381 306 859 687 249 1596 773 635 240 562 > ENSMUSG00000002015 399 956 531 1725 1217 1111 668 928 350 549 828 2199 480 702 1611 1448 331 678 1199 1014 652 913 > > >design > (Intercept) strain CSD > 1 1 0 0 > 2 1 0 0 > 3 1 0 0 > 4 1 0 0 > 5 1 0 0 > 6 1 0 0 > 7 1 0 1 > 8 1 0 1 > 9 1 0 1 > 10 1 0 1 > 11 1 0 1 > 12 1 0 1 > 13 1 1 0 > 14 1 1 0 > 15 1 1 0 > 16 1 1 0 > 17 1 1 0 > 18 1 1 0 > 19 1 1 1 > 20 1 1 1 > 21 1 1 1 > 22 1 1 1 > > > >d <- DGEList(data_files, lib.size=colSums(data_files)) > An object of class "DGEList" > $samples > group lib.size norm.factors > WT_SHAM1 1 6154923 1 > WT_SHAM2 1 12269537 1 > WT_SHAM3 1 8785094 1 > WT_SHAM4 1 19878567 1 > WT_SHAM5 1 13420516 1 > 17 more rows ... > > $counts > WT_SHAM1 WT_SHAM2 WT_SHAM3 WT_SHAM4 WT_SHAM5 WT_SHAM6 WT_CSD1 WT_CSD2 WT_CSD3 WT_CSD4 WT_CSD5 WT_CSD6 RQ_SHAM1 RQ_SHAM2 RQ_SHAM3 RQ_SHAM4 RQ_SHAM5 RQ_SHAM6 RQ_CSD1 RQ_CSD2 RQ_CSD3 RQ_CSD4 > ENSMUSG00000002012 553 1167 660 1736 365 760 971 961 974 1790 1458 2843 556 871 1263 1142 1043 1919 969 794 771 682 > ENSMUSG00000028182 2 11 3 8 2 8 1 10 3 39 5 19 1 5 34 13 1 3 8 13 5 1 > ENSMUSG00000002017 26 50 50 42 100 140 29 31 41 69 147 99 20 43 74 135 63 92 55 44 23 68 > ENSMUSG00000028184 381 664 442 762 476 653 618 376 353 806 1271 1938 381 306 859 687 249 1596 773 635 240 562 > ENSMUSG00000002015 399 956 531 1725 1217 1111 668 928 350 549 828 2199 480 702 1611 1448 331 678 1199 1014 652 913 > 23841 more rows ... > > $all.zeros > ENSMUSG00000002012 ENSMUSG00000028182 ENSMUSG00000002017 ENSMUSG00000028184 ENSMUSG00000002015 > FALSE FALSE FALSE FALSE FALSE > 23841 more elements ... > > >d <- calcNormFactors(d) > An object of class "DGEList" > $samples > group lib.size norm.factors > WT_SHAM1 1 6154923 0.9765708 > WT_SHAM2 1 12269537 0.9914651 > WT_SHAM3 1 8785094 0.9693995 > WT_SHAM4 1 19878567 0.9193010 > WT_SHAM5 1 13420516 1.0142604 > 17 more rows ... > > $counts > WT_SHAM1 WT_SHAM2 WT_SHAM3 WT_SHAM4 WT_SHAM5 WT_SHAM6 WT_CSD1 WT_CSD2 WT_CSD3 WT_CSD4 WT_CSD5 WT_CSD6 RQ_SHAM1 RQ_SHAM2 RQ_SHAM3 RQ_SHAM4 RQ_SHAM5 RQ_SHAM6 RQ_CSD1 RQ_CSD2 RQ_CSD3 RQ_CSD4 > ENSMUSG00000002012 553 1167 660 1736 365 760 971 961 974 1790 1458 2843 556 871 1263 1142 1043 1919 969 794 771 682 > ENSMUSG00000028182 2 11 3 8 2 8 1 10 3 39 5 19 1 5 34 13 1 3 8 13 5 1 > ENSMUSG00000002017 26 50 50 42 100 140 29 31 41 69 147 99 20 43 74 135 63 92 55 44 23 68 > ENSMUSG00000028184 381 664 442 762 476 653 618 376 353 806 1271 1938 381 306 859 687 249 1596 773 635 240 562 > ENSMUSG00000002015 399 956 531 1725 1217 1111 668 928 350 549 828 2199 480 702 1611 1448 331 678 1199 1014 652 913 > 23841 more rows ... > > $all.zeros > ENSMUSG00000002012 ENSMUSG00000028182 ENSMUSG00000002017 ENSMUSG00000028184 ENSMUSG00000002015 > FALSE FALSE FALSE FALSE FALSE > 23841 more elements ... > > > >d <- estimateGLMCommonDisp(d, design=design) > $common.dispersion > [1] 0.2005023 > > > d <- estimateGLMTrendedDisp(d, design=design) > Error in cutWithMinN(abundance[!all.zero], intervals = nbins, min.n = min.n) : > function has failed, perhaps because of too many tied values? > > -- output of sessionInfo(): > >> sessionInfo() > R version 2.14.2 (2012-02-29) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252 LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C > [5] LC_TIME=Dutch_Netherlands.1252 > > attached base packages: > [1] splines stats graphics grDevices utils datasets methods base > > other attached packages: > [1] edgeR_2.4.6 limma_3.10.3 > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}