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 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 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 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" 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]" >>>>>> 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]]