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Hi Jason, Thanks for the hint. You were correct. Apparently no genes passes the p-value threshold of 0.05, which is to be expected, when doing an analysis of only two samples with no replica. I didn't think about that factor, as the error message is very encrypted. I think there should be a better message there - something like " no genes passes the threshhold of the given p-value". This should be checked, before the command try to convert the 'fit' Object into a data.frame with no genes in it and than do the images. Anyhow, thanks again for this (obvious :( ) comment Assa On Thu, Jun 12, 2014 at 12:20 AM, Jason Hackney <hackney.jason@gene.com> wrote: > Hi Assa, > > A couple of questions/comments: > > 1. How many features pass your p-value cutoff of 0.05? > 2. Could you provide your sessionInfo, so I can see what version of > ReportingTools you're using? > > I believe the data.frame in the error message comes from the coercion of > your DESeqResults object to a data.frame before being formatted as an html > table. This happens in two steps for this type of object: First, the > results are made into a data.frame, optionally including annotations (using > the toReportDF method); second, plots and optionally links are added to the > data.frame (using the modifyReportDF method). > > My further guess about what's going wrong here is that there is something > going wrong in making the plots for the individual genes. You could test > this by adding the parameter make.plots = FALSE to your publish call. > This might not throw the same error. > > At the very least, it looks like there's a bug in the modifyReportDF > method(s) being used that don't correctly check for zero row input, so I'll > include a fix for that with a more helpful error. > > Thanks! > > J > > > > > > On Wed, Jun 11, 2014 at 1:31 PM, Assa Yeroslaviz <frymor@gmail.com> wrote: > >> Hi, >> >> I am running (again) a DESeq analysis and try to create a html report >> using >> the ReportingTools package. >> >> I do the DESeq2 analysis and get the fit object like in the manual (see >> below). I than try to create the html report but keep getting an error I >> can't interpret. >> >> Error in `$<-.data.frame`(`*tmp*`, "Image", value = "> href=\"figuresDEgenes_IFM_0_3dvsleg/boxplot..pdf\">> src=\"figuresDEgenes_IFM_0_3dvsleg/mini..png\" >> alt=\"figuresDEgenes_IFM_0_3dvsleg/mini..png\">") : >> replacement has 1 row, data has 0 >> >> I really don't understand what data.frame is meant here. >> >> In the DEseq analysis I don't have any replica, only two samples, which I >> ran with this code: >> FirstComp <- Table[,c(5,8)] >> > head(FirstComp) >> WT treated >> FBgn0000003 0 7 >> FBgn0000008 92 2096 >> FBgn0000014 32 23 >> FBgn0000015 13 21 >> FBgn0000017 652 2782 >> FBgn0000018 51 139 >> colData1 <- data.frame(row.names=names(FirstComp), condition = c("WT", >> "treated")) >> >> cds <- DESeqDataSetFromMatrix ( >> countData = FirstComp, >> colData = colData1, >> design = ~ condition >> ) >> >> class: DESeqDataSet >> dim: 14869 2 >> exptData(0): >> assays(1): counts >> rownames(14869): FBgn0000003 FBgn0000008 ... FBgn0261574 FBgn0261575 >> rowData metadata column names(0): >> colnames(2): WT treated >> colData names(1): condition >> >> fit = DESeq(cds) >> res = results(fit) >> >> After that I try to create the html report with these commands: >> des2Report <- HTMLReport() >> publish(fit,des2Report, pvalueCutoff=0.05,annotation.db=NULL, factor = >> colData(fit)$condition) >> finish(des2Report) >> >> Than I keep getting the above mentioned error message. >> >> Can anyone explain to me what I am doing wrong? >> >> thanks >> Assa >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > Jason A. Hackney, Ph.D. > Bioinformatics and Computational Biology > Genentech > hackney.jason@gene.com > 650-467-5084 > > > [[alternative HTML version deleted]]