[BioC] R EdgeR package error
Gordon K Smyth
smyth at wehi.EDU.AU
Sat Nov 3 07:56:56 CET 2012
Dear Lisannne,
Please have a closer look at the posting guide
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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
>
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