Error message with DESeqDataSet
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Hi Mike, I have a small technical question. I kept getting this error message when I tried running a DE with DESq2 (version 1.2.6): DESeqDataSet(se, design = design) : some values in assay are negative It does not make sense to me because there is no negative values in the dataset (gene count). Please explain. Thank you, Yoong -- output of sessionInfo(): > dds = DESeqDataSetFromMatrix(countData = DEAnatomy, colData = colData, design = ~genotype+time+temp) Error in DESeqDataSet(se, design = design) : some values in assay are negative -- Sent via the guest posting facility at bioconductor.org.
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Hi Yoong, The test that prints this error is simply: if ( any( counts(object) < 0 ) ) return( "the count data contains negative values" ) What do you get for: any( DEAnatomy < 0 ) Can you include the output of sessionInfo() ? Mike On Mar 4, 2014 7:49 PM, "Yoong [guest]" <guest@bioconductor.org> wrote: > > Hi Mike, > > I have a small technical question. I kept getting this error message when > I tried running a DE with DESq2 (version 1.2.6): > > DESeqDataSet(se, design = design) : > some values in assay are negative > > It does not make sense to me because there is no negative values in the > dataset (gene count). Please explain. > > Thank you, > Yoong > > -- output of sessionInfo(): > > > dds = DESeqDataSetFromMatrix(countData = DEAnatomy, colData = colData, > design = ~genotype+time+temp) > Error in DESeqDataSet(se, design = design) : > some values in assay are negative > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
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Hi Mike, Hre you go: > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] DESeq2_1.2.6 RcppArmadillo_0.3.920.3 Rcpp_0.10.6 [4] GenomicRanges_1.14.3 XVector_0.2.0 IRanges_1.20.6 [7] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] annotate_1.40.0 AnnotationDbi_1.24.0 Biobase_2.22.0 [4] DBI_0.2-7 genefilter_1.44.0 grid_3.0.2 [7] lattice_0.20-23 locfit_1.5-9.1 RColorBrewer_1.0-5 [10] RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 [13] survival_2.37-4 tools_3.0.2 XML_3.98-1.1 [16] xtable_1.7-1 Thank you, Yoong On Tue, Mar 4, 2014 at 7:33 PM, Michael Love <michaelisaiahlove@gmail.com>wrote: > Hi Yoong, > > The test that prints this error is simply: > > if ( any( counts(object) < 0 ) ) > return( "the count data contains negative values" ) > > What do you get for: > > any( DEAnatomy < 0 ) > > Can you include the output of sessionInfo() ? > > Mike > On Mar 4, 2014 7:49 PM, "Yoong [guest]" <guest@bioconductor.org> wrote: > >> >> Hi Mike, >> >> I have a small technical question. I kept getting this error message when >> I tried running a DE with DESq2 (version 1.2.6): >> >> DESeqDataSet(se, design = design) : >> some values in assay are negative >> >> It does not make sense to me because there is no negative values in the >> dataset (gene count). Please explain. >> >> Thank you, >> Yoong >> >> -- output of sessionInfo(): >> >> > dds = DESeqDataSetFromMatrix(countData = DEAnatomy, colData = colData, >> design = ~genotype+time+temp) >> Error in DESeqDataSet(se, design = design) : >> some values in assay are negative >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> > [[alternative HTML version deleted]]
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What do you get for: any( DEAnatomy < 0 ) On Mar 5, 2014 11:45 AM, "FeiYian Yoong" <fyoong@ucdavis.edu> wrote: > Hi Mike, > > Hre you go: > > > sessionInfo() R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] DESeq2_1.2.6 RcppArmadillo_0.3.920.3 Rcpp_0.10.6 > [4] GenomicRanges_1.14.3 XVector_0.2.0 IRanges_1.20.6 > [7] BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] annotate_1.40.0 AnnotationDbi_1.24.0 Biobase_2.22.0 > [4] DBI_0.2-7 genefilter_1.44.0 grid_3.0.2 > [7] lattice_0.20-23 locfit_1.5-9.1 RColorBrewer_1.0-5 > [10] RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 > [13] survival_2.37-4 tools_3.0.2 XML_3.98-1.1 > [16] xtable_1.7-1 > > > Thank you, > > > Yoong > > > > > On Tue, Mar 4, 2014 at 7:33 PM, Michael Love <michaelisaiahlove@gmail.com>wrote: > >> Hi Yoong, >> >> The test that prints this error is simply: >> >> if ( any( counts(object) < 0 ) ) >> return( "the count data contains negative values" ) >> >> What do you get for: >> >> any( DEAnatomy < 0 ) >> >> Can you include the output of sessionInfo() ? >> >> Mike >> On Mar 4, 2014 7:49 PM, "Yoong [guest]" <guest@bioconductor.org> wrote: >> >>> >>> Hi Mike, >>> >>> I have a small technical question. I kept getting this error message >>> when I tried running a DE with DESq2 (version 1.2.6): >>> >>> DESeqDataSet(se, design = design) : >>> some values in assay are negative >>> >>> It does not make sense to me because there is no negative values in the >>> dataset (gene count). Please explain. >>> >>> Thank you, >>> Yoong >>> >>> -- output of sessionInfo(): >>> >>> > dds = DESeqDataSetFromMatrix(countData = DEAnatomy, colData = colData, >>> design = ~genotype+time+temp) >>> Error in DESeqDataSet(se, design = design) : >>> some values in assay are negative >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >> > [[alternative HTML version deleted]]
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Hi Mike, I am not sure what you are asking for. I tried any( DEAnatomy < 0 ) and I got a warning message Warning message:In Ops.factor(left, right) : < not meaningful for factors Please clarify your question so that I can provide you with relevant information. Many thanks, Yoong On Wed, Mar 5, 2014 at 9:22 AM, Michael Love <michaelisaiahlove@gmail.com>wrote: > What do you get for: > > any( DEAnatomy < 0 ) > On Mar 5, 2014 11:45 AM, "FeiYian Yoong" <fyoong@ucdavis.edu> wrote: > >> Hi Mike, >> >> Hre you go: >> >> > sessionInfo() R version 3.0.2 (2013-09-25) >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 >> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] DESeq2_1.2.6 RcppArmadillo_0.3.920.3 Rcpp_0.10.6 >> [4] GenomicRanges_1.14.3 XVector_0.2.0 IRanges_1.20.6 >> [7] BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.40.0 AnnotationDbi_1.24.0 Biobase_2.22.0 >> [4] DBI_0.2-7 genefilter_1.44.0 grid_3.0.2 >> [7] lattice_0.20-23 locfit_1.5-9.1 RColorBrewer_1.0-5 >> [10] RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 >> [13] survival_2.37-4 tools_3.0.2 XML_3.98-1.1 >> [16] xtable_1.7-1 >> >> >> Thank you, >> >> >> Yoong >> >> >> >> >> On Tue, Mar 4, 2014 at 7:33 PM, Michael Love <michaelisaiahlove@gmail.com>> > wrote: >> >>> Hi Yoong, >>> >>> The test that prints this error is simply: >>> >>> if ( any( counts(object) < 0 ) ) >>> return( "the count data contains negative values" ) >>> >>> What do you get for: >>> >>> any( DEAnatomy < 0 ) >>> >>> Can you include the output of sessionInfo() ? >>> >>> Mike >>> On Mar 4, 2014 7:49 PM, "Yoong [guest]" <guest@bioconductor.org> wrote: >>> >>>> >>>> Hi Mike, >>>> >>>> I have a small technical question. I kept getting this error message >>>> when I tried running a DE with DESq2 (version 1.2.6): >>>> >>>> DESeqDataSet(se, design = design) : >>>> some values in assay are negative >>>> >>>> It does not make sense to me because there is no negative values in the >>>> dataset (gene count). Please explain. >>>> >>>> Thank you, >>>> Yoong >>>> >>>> -- output of sessionInfo(): >>>> >>>> > dds = DESeqDataSetFromMatrix(countData = DEAnatomy, colData = >>>> colData, design = ~genotype+time+temp) >>>> Error in DESeqDataSet(se, design = design) : >>>> some values in assay are negative >>>> >>>> -- >>>> Sent via the guest posting facility at bioconductor.org. >>>> >>> >> [[alternative HTML version deleted]]
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hi Yoong, It appears that DEAnatomy is not a matrix of integers but factors. DESeqDataSetFromMatrix() is expecting a matrix of non-negative integers for the 'countData' argument. you can explore with: class(DEAnatomy) str(DEAnatomy) head(DEAnatomy) Can you provide the code you used to make or import DEAnatomy? Mike On Wed, Mar 5, 2014 at 7:34 PM, FeiYian Yoong <fyoong@ucdavis.edu> wrote: > Hi Mike, > > I am not sure what you are asking for. I tried any( DEAnatomy < 0 ) and I > got a warning message > > Warning message:In Ops.factor(left, right) : < not meaningful for factors > > Please clarify your question so that I can provide you with relevant information. > > Many thanks, > > Yoong > > > > On Wed, Mar 5, 2014 at 9:22 AM, Michael Love <michaelisaiahlove@gmail.com>wrote: > >> What do you get for: >> >> any( DEAnatomy < 0 ) >> On Mar 5, 2014 11:45 AM, "FeiYian Yoong" <fyoong@ucdavis.edu> wrote: >> >>> Hi Mike, >>> >>> Hre you go: >>> >>> >>> > sessionInfo() R version 3.0.2 (2013-09-25) >>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>> >>> locale: >>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 >>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C >>> [5] LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] parallel stats graphics grDevices utils datasets methods >>> [8] base >>> >>> other attached packages: >>> [1] DESeq2_1.2.6 RcppArmadillo_0.3.920.3 Rcpp_0.10.6 >>> [4] GenomicRanges_1.14.3 XVector_0.2.0 IRanges_1.20.6 >>> [7] BiocGenerics_0.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] annotate_1.40.0 AnnotationDbi_1.24.0 Biobase_2.22.0 >>> [4] DBI_0.2-7 genefilter_1.44.0 grid_3.0.2 >>> [7] lattice_0.20-23 locfit_1.5-9.1 RColorBrewer_1.0-5 >>> [10] RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 >>> [13] survival_2.37-4 tools_3.0.2 XML_3.98-1.1 >>> [16] xtable_1.7-1 >>> >>> >>> >>> Thank you, >>> >>> >>> >>> Yoong >>> >>> >>> >>> >>> On Tue, Mar 4, 2014 at 7:33 PM, Michael Love < >>> michaelisaiahlove@gmail.com> wrote: >>> >>>> Hi Yoong, >>>> >>>> The test that prints this error is simply: >>>> >>>> if ( any( counts(object) < 0 ) ) >>>> return( "the count data contains negative values" ) >>>> >>>> What do you get for: >>>> >>>> any( DEAnatomy < 0 ) >>>> >>>> Can you include the output of sessionInfo() ? >>>> >>>> Mike >>>> On Mar 4, 2014 7:49 PM, "Yoong [guest]" <guest@bioconductor.org> wrote: >>>> >>>>> >>>>> Hi Mike, >>>>> >>>>> I have a small technical question. I kept getting this error message >>>>> when I tried running a DE with DESq2 (version 1.2.6): >>>>> >>>>> DESeqDataSet(se, design = design) : >>>>> some values in assay are negative >>>>> >>>>> It does not make sense to me because there is no negative values in >>>>> the dataset (gene count). Please explain. >>>>> >>>>> Thank you, >>>>> Yoong >>>>> >>>>> -- output of sessionInfo(): >>>>> >>>>> > dds = DESeqDataSetFromMatrix(countData = DEAnatomy, colData = >>>>> colData, design = ~genotype+time+temp) >>>>> Error in DESeqDataSet(se, design = design) : >>>>> some values in assay are negative >>>>> >>>>> -- >>>>> Sent via the guest posting facility at bioconductor.org. >>>>> >>>> >>> > [[alternative HTML version deleted]]
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hi Yoong, Note that one column of DEAnatomy contains strings, so read.table() turns this column into a factor. You should investigate why this column of this file has non numeric values. Mike On Wed, Mar 5, 2014 at 9:42 PM, Michael Love <michaelisaiahlove@gmail.com>wrote: > hi Yoong, > > It appears that DEAnatomy is not a matrix of integers but factors. DESeqDataSetFromMatrix() > is expecting a matrix of non-negative integers for the 'countData' argument. > > you can explore with: > > class(DEAnatomy) > str(DEAnatomy) > head(DEAnatomy) > > Can you provide the code you used to make or import DEAnatomy? > > Mike > > > On Wed, Mar 5, 2014 at 7:34 PM, FeiYian Yoong <fyoong@ucdavis.edu> wrote: > >> Hi Mike, >> >> I am not sure what you are asking for. I tried any( DEAnatomy < 0 ) and I >> got a warning message >> >> Warning message:In Ops.factor(left, right) : < not meaningful for factors >> >> Please clarify your question so that I can provide you with relevant information. >> >> Many thanks, >> >> Yoong >> >> >> >> On Wed, Mar 5, 2014 at 9:22 AM, Michael Love <michaelisaiahlove@gmail.com>> > wrote: >> >>> What do you get for: >>> >>> any( DEAnatomy < 0 ) >>> On Mar 5, 2014 11:45 AM, "FeiYian Yoong" <fyoong@ucdavis.edu> wrote: >>> >>>> Hi Mike, >>>> >>>> Hre you go: >>>> >>>> >>>> > sessionInfo() R version 3.0.2 (2013-09-25) >>>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>>> >>>> locale: >>>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 >>>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C >>>> [5] LC_TIME=English_United States.1252 >>>> >>>> attached base packages: >>>> [1] parallel stats graphics grDevices utils datasets methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] DESeq2_1.2.6 RcppArmadillo_0.3.920.3 Rcpp_0.10.6 >>>> [4] GenomicRanges_1.14.3 XVector_0.2.0 IRanges_1.20.6 >>>> [7] BiocGenerics_0.8.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] annotate_1.40.0 AnnotationDbi_1.24.0 Biobase_2.22.0 >>>> [4] DBI_0.2-7 genefilter_1.44.0 grid_3.0.2 >>>> [7] lattice_0.20-23 locfit_1.5-9.1 RColorBrewer_1.0-5 >>>> [10] RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 >>>> [13] survival_2.37-4 tools_3.0.2 XML_3.98-1.1 >>>> [16] xtable_1.7-1 >>>> >>>> >>>> >>>> Thank you, >>>> >>>> >>>> >>>> Yoong >>>> >>>> >>>> >>>> >>>> On Tue, Mar 4, 2014 at 7:33 PM, Michael Love < >>>> michaelisaiahlove@gmail.com> wrote: >>>> >>>>> Hi Yoong, >>>>> >>>>> The test that prints this error is simply: >>>>> >>>>> if ( any( counts(object) < 0 ) ) >>>>> return( "the count data contains negative values" ) >>>>> >>>>> What do you get for: >>>>> >>>>> any( DEAnatomy < 0 ) >>>>> >>>>> Can you include the output of sessionInfo() ? >>>>> >>>>> Mike >>>>> On Mar 4, 2014 7:49 PM, "Yoong [guest]" <guest@bioconductor.org> >>>>> wrote: >>>>> >>>>>> >>>>>> Hi Mike, >>>>>> >>>>>> I have a small technical question. I kept getting this error message >>>>>> when I tried running a DE with DESq2 (version 1.2.6): >>>>>> >>>>>> DESeqDataSet(se, design = design) : >>>>>> some values in assay are negative >>>>>> >>>>>> It does not make sense to me because there is no negative values in >>>>>> the dataset (gene count). Please explain. >>>>>> >>>>>> Thank you, >>>>>> Yoong >>>>>> >>>>>> -- output of sessionInfo(): >>>>>> >>>>>> > dds = DESeqDataSetFromMatrix(countData = DEAnatomy, colData = >>>>>> colData, design = ~genotype+time+temp) >>>>>> Error in DESeqDataSet(se, design = design) : >>>>>> some values in assay are negative >>>>>> >>>>>> -- >>>>>> Sent via the guest posting facility at bioconductor.org. >>>>>> >>>>> >>>> >> > [[alternative HTML version deleted]]
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Hi Mike, I found the non-integer in that column. Thanks so much for your time and help! Yoong On Thu, Mar 6, 2014 at 7:35 AM, Michael Love <michaelisaiahlove@gmail.com>wrote: > hi Yoong, > > Note that one column of DEAnatomy contains strings, so read.table() turns > this column into a factor. You should investigate why this column of this > file has non numeric values. > > Mike > > > On Wed, Mar 5, 2014 at 9:42 PM, Michael Love <michaelisaiahlove@gmail.com>wrote: > >> hi Yoong, >> >> It appears that DEAnatomy is not a matrix of integers but factors. DESeqDataSetFromMatrix() >> is expecting a matrix of non-negative integers for the 'countData' argument. >> >> you can explore with: >> >> class(DEAnatomy) >> str(DEAnatomy) >> head(DEAnatomy) >> >> Can you provide the code you used to make or import DEAnatomy? >> >> Mike >> >> >> On Wed, Mar 5, 2014 at 7:34 PM, FeiYian Yoong <fyoong@ucdavis.edu> wrote: >> >>> Hi Mike, >>> >>> I am not sure what you are asking for. I tried any( DEAnatomy < 0 ) and >>> I got a warning message >>> >>> Warning message:In Ops.factor(left, right) : < not meaningful for factors >>> >>> Please clarify your question so that I can provide you with relevant information. >>> >>> Many thanks, >>> >>> Yoong >>> >>> >>> >>> On Wed, Mar 5, 2014 at 9:22 AM, Michael Love < >>> michaelisaiahlove@gmail.com> wrote: >>> >>>> What do you get for: >>>> >>>> any( DEAnatomy < 0 ) >>>> On Mar 5, 2014 11:45 AM, "FeiYian Yoong" <fyoong@ucdavis.edu> wrote: >>>> >>>>> Hi Mike, >>>>> >>>>> Hre you go: >>>>> >>>>> >>>>> > sessionInfo() R version 3.0.2 (2013-09-25) >>>>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>>>> >>>>> locale: >>>>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 >>>>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C >>>>> [5] LC_TIME=English_United States.1252 >>>>> >>>>> attached base packages: >>>>> [1] parallel stats graphics grDevices utils datasets methods >>>>> [8] base >>>>> >>>>> other attached packages: >>>>> [1] DESeq2_1.2.6 RcppArmadillo_0.3.920.3 Rcpp_0.10.6 >>>>> [4] GenomicRanges_1.14.3 XVector_0.2.0 IRanges_1.20.6 >>>>> [7] BiocGenerics_0.8.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] annotate_1.40.0 AnnotationDbi_1.24.0 Biobase_2.22.0 >>>>> [4] DBI_0.2-7 genefilter_1.44.0 grid_3.0.2 >>>>> [7] lattice_0.20-23 locfit_1.5-9.1 RColorBrewer_1.0-5 >>>>> [10] RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 >>>>> [13] survival_2.37-4 tools_3.0.2 XML_3.98-1.1 >>>>> [16] xtable_1.7-1 >>>>> >>>>> >>>>> >>>>> Thank you, >>>>> >>>>> >>>>> >>>>> Yoong >>>>> >>>>> >>>>> >>>>> >>>>> On Tue, Mar 4, 2014 at 7:33 PM, Michael Love < >>>>> michaelisaiahlove@gmail.com> wrote: >>>>> >>>>>> Hi Yoong, >>>>>> >>>>>> The test that prints this error is simply: >>>>>> >>>>>> if ( any( counts(object) < 0 ) ) >>>>>> return( "the count data contains negative values" ) >>>>>> >>>>>> What do you get for: >>>>>> >>>>>> any( DEAnatomy < 0 ) >>>>>> >>>>>> Can you include the output of sessionInfo() ? >>>>>> >>>>>> Mike >>>>>> On Mar 4, 2014 7:49 PM, "Yoong [guest]" <guest@bioconductor.org> >>>>>> wrote: >>>>>> >>>>>>> >>>>>>> Hi Mike, >>>>>>> >>>>>>> I have a small technical question. I kept getting this error message >>>>>>> when I tried running a DE with DESq2 (version 1.2.6): >>>>>>> >>>>>>> DESeqDataSet(se, design = design) : >>>>>>> some values in assay are negative >>>>>>> >>>>>>> It does not make sense to me because there is no negative values in >>>>>>> the dataset (gene count). Please explain. >>>>>>> >>>>>>> Thank you, >>>>>>> Yoong >>>>>>> >>>>>>> -- output of sessionInfo(): >>>>>>> >>>>>>> > dds = DESeqDataSetFromMatrix(countData = DEAnatomy, colData = >>>>>>> colData, design = ~genotype+time+temp) >>>>>>> Error in DESeqDataSet(se, design = design) : >>>>>>> some values in assay are negative >>>>>>> >>>>>>> -- >>>>>>> Sent via the guest posting facility at bioconductor.org. >>>>>>> >>>>>> >>>>> >>> >> > [[alternative HTML version deleted]]
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