ReportingTools error message
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Assa Yeroslaviz ★ 1.5k
@assa-yeroslaviz-1597
Last seen 10 days ago
Munich, Germany
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 `$<-.data.frame`(`*tmp*`, "Image", value = "\"figuresDEgenes_IFM_0_3dvsleg/mini..png\"") : replacement has 1 row, data has 0 I really don't understand what data.frame is meant here. In the DEseq analysis I don't have any replica, only two samples, which I ran with this code: FirstComp <- Table[,c(5,8)] > head(FirstComp) WT treated FBgn0000003 0 7 FBgn0000008 92 2096 FBgn0000014 32 23 FBgn0000015 13 21 FBgn0000017 652 2782 FBgn0000018 51 139 colData1 <- data.frame(row.names=names(FirstComp), condition = c("WT", "treated")) cds <- DESeqDataSetFromMatrix ( countData = FirstComp, colData = colData1, design = ~ condition ) class: DESeqDataSet dim: 14869 2 exptData(0): assays(1): counts rownames(14869): FBgn0000003 FBgn0000008 ... FBgn0261574 FBgn0261575 rowData metadata column names(0): colnames(2): WT treated colData names(1): condition fit = DESeq(cds) res = results(fit) After that I try to create the html report with these commands: des2Report <- HTMLReport() publish(fit,des2Report, pvalueCutoff=0.05,annotation.db=NULL, factor = colData(fit)$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]]
DESeq ReportingTools DESeq2 DESeq ReportingTools DESeq2 • 1.1k views
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Assa Yeroslaviz ★ 1.5k
@assa-yeroslaviz-1597
Last seen 10 days ago
Munich, Germany
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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]]
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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]]
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