User: n.tear

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n.tear20
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Posts by n.tear

<prev • 25 results • page 1 of 3 • next >
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How to colour all points that agree with multiple conditions
... Hello, I am trying to make an MA plot of all the genes and colour in red all those that have a padj value of <0.05 AND have a >1 OR <-1 LFC I cant find what syntax to use res.sLFCdf ggplot(res.sLFCdf, aes(x = log2(baseMean), y=log2FoldChange, col= res.sIHW$padj<0.05 & ...
R rna-seq written 28 days ago by n.tear20 • updated 28 days ago by caggtaagtat1.0k
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Comment: C: Error in `[.data.frame`(res.df, , cols) : undefined columns selected when export
... Hi Kevin, Thanks for your help. Ive done exacly as you have said above and managed to work it out in the end. Cheers Nathan ...
written 28 days ago by n.tear20
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Best values to report. svalues? padj values? IHW results values? apeglm shrinkage values?
... Hi, I have run an RNAseq analysis and am stuck on what would be the most appropriate thing to report in results. I first decided to report the results of IHW tested results from DESeq2, from reading the vignettes this output is suggested to be a better method than the default results output by DES ...
apeglm rna-seq written 28 days ago by n.tear20 • updated 28 days ago by Kevin Blighe61k
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Comment: C: Error in `[.data.frame`(res.df, , cols) : undefined columns selected when export
... Yes looked in exel and no missing values and checked the class of each column in res.sLFCdf and they are correct could it be an issue that not all the rownames of res.s are in org.Hs.eg.db when I make the anno? > library(org.Hs.eg.db) > res.s$symbol <- mapIds(org.Hs.eg.db,keys = r ...
written 4 weeks ago by n.tear20
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Comment: C: Error in `[.data.frame`(res.df, , cols) : undefined columns selected when export
... output suggests not > table( is.na(res.sLFCdf$logmean) ) FALSE 31172 > table( res.sLFCdf$logmean == 'Inf' ) FALSE 31172 ...
written 4 weeks ago by n.tear20
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Comment: C: Error in `[.data.frame`(res.df, , cols) : undefined columns selected when export
... Hi Kevin, many thanks for your continued support. Unfortunately I am still having no luck > res.sLFCdf$logmean <- log(res.sLFCdf$baseMean + 1) > glMDPlot(res.sLFCdf, xval <- 'logmean', yval <- 'log2FoldChange', + status=status, counts=counts(dds.s,normalized=T ...
written 4 weeks ago by n.tear20
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Comment: C: Error in `[.data.frame`(res.df, , cols) : undefined columns selected when export
... I generated the res.sLFC using: res.sLFC <- lfcShrink(dds.s, coef="co", type="apeglm", lfcThreshold=2) As a data frame: > res.sLFCdf <- as.data.frame(res.sLFC) > res.sLFCdf baseMean log2FoldChange lfcSE svalue ENSG00000000003 3.089928 ...
written 5 weeks ago by n.tear20
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Comment: C: Error in `[.data.frame`(res.df, , cols) : undefined columns selected when export
... Hi Kevin thank you for your reply str(res.sLFC) Formal class 'DESeqResults' [package "DESeq2"] with 7 slots ..@ priorInfo :List of 4 .. ..$ type : chr "apeglm" .. ..$ package : chr "apeglm" .. ..$ version :Classes 'packa ...
written 5 weeks ago by n.tear20
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Error in `[.data.frame`(res.df, , cols) : undefined columns selected when exporting glimma
... Hi, I am trying to export my RNAseq results with glimma and I am following this workshop (https://bioconductor.github.io/BiocWorkshops/rna-seq-data-analysis-with-deseq2.html#building-reports) unfortuneatly I am geting an error as per the title. Please would someone be able to educate me as to why ...
rna-seq written 5 weeks ago by n.tear20
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Comment: C: Generating heatmaps of pre-selected candidate genes after deseq2
... Hi, did you solve this? I want to do a similar thing with a number of candidate genes but using rlog data to include in a pheatmap ...
written 10 weeks ago by n.tear20

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