User: mictadlo

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mictadlo0
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Posts by mictadlo

<prev • 48 results • page 1 of 5 • next >
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Answer: A: gene names disapper from heatmap.2 after adding gene descripton
... I think I found the solution rownames(logCPM) <- as.character(row.names(y)). ...
written 5 weeks ago by mictadlo0
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gene names disapper from heatmap.2 after adding gene descripton
... Hi, after I added gene description to y <- DGEList(counts=rawCountTable, group=group, genes = merged.descriptions) the gene names have replaced by numbers > logCPM <- cpm(y, prior.count=2, log=TRUE) > head(y$genes) gene_name gene_description 3 sp000 ...
edger heatmap.2 written 5 weeks ago by mictadlo0
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Comment: C: Error in plot.new() : figure margins too large
... Thank you for pointing out that it is a CRAN package. ...
written 5 weeks ago by mictadlo0
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Error in plot.new() : figure margins too large
... Hi, I got Error in plot.new() : figure margins too large with the below code: > logCPM <- cpm(y, prior.count=2, log=TRUE) > head(y$genes) gene_name gene_description 3 sp0000003 <NA> 4 sp0000004 ...
edger written 5 weeks ago by mictadlo0 • updated 5 weeks ago by Gordon Smyth32k
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Comment: C: saving a plot as png and also showing inside Rstudio
... You mean I have to run it twice? ...
written 5 weeks ago by mictadlo0
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saving a plot as png and also showing inside Rstudio
... Hi, the following plot get saved as png but it does not show up inside Rstudio. png("~/sampledata.png") x <- matrix(rnorm(1000*6,sd=sd),1000,6) rownames(x) <- paste("Gene",1:1000) x[1:50,4:6] <- x[1:50,4:6] + 2 ## capture par settings, then add space to the right opar <- par(no.readonly ...
edger ggplot2 written 6 weeks ago by mictadlo0 • updated 6 weeks ago by Aaron Lun17k
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How is it possible to get a legend outside plotMDS?
... How is it possible to get a legend outside plotMDS? pch <- c(0,1,2,15,16,17) colors <- rep(c("darkgreen", "red", "blue"), 2) plotMDS(y, col=colors[group], pch=pch[group]) legend("topleft", legend=levels(group), pch=pch, col=colors, ncol=2) Thank you in advance. ...
edger ggplot2 written 6 weeks ago by mictadlo0 • updated 6 weeks ago by James W. MacDonald45k
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Comment: C: adding a description column to glmTreat output
... Will I lose the gene name column by assign gene.description to y$genes if yes then is there a way to keep both? ...
written 6 weeks ago by mictadlo0
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How to filter glmTreat results by a false discovery rate (FDR) of 0.05
... Hello, Currenty, I call glmTreat method as following: tr <- glmTreat(fit, contrast=B.LvsP, coef = 2, lfc=log2(1.5)) topTags(tr) I discovered this paper and In the "Differential gene and microRNA expression" section they described that the differentially expressed genes (DEGs) were filtered us ...
edger written 6 weeks ago by mictadlo0 • updated 6 weeks ago by Aaron Lun17k
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adding a description column to glmTreat output
... Hi, Below is my current code: y <- DGEList(counts=rawCountTable, group=group, genes = rownames(rawCountTable)) > head(y$samples) group lib.size norm.factors X1916.MJO.0001_1 Root_tip.1.5 33986982 0.9543329 X1916.MJO.0002_1 Root_tip.1.5 31781171 0.8787148 X1916.MJ ...
edger written 6 weeks ago by mictadlo0 • updated 6 weeks ago by Aaron Lun17k

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