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 13 months 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$genes) gene_name gene_description 3 sp000 ...
edger heatmap.2 written 13 months ago by mictadlo0
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Comment: C: Error in plot.new() : figure margins too large
... Thank you for pointing out that it is a CRAN package. ...
written 13 months ago by mictadlo0
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Error in plot.new() : figure margins too large
... Hi, I got Error in plot.new() : figure margins too large with the below code: > logCPM <- cpm(y, prior.count=2, log=TRUE) > head(y$genes) gene_name gene_description 3 sp0000003 <NA> 4 sp0000004 ...
edger written 13 months ago by mictadlo0 • updated 13 months ago by Gordon Smyth35k
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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 13 months 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 13 months ago by mictadlo0 • updated 13 months ago by Aaron Lun21k
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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 13 months ago by mictadlo0 • updated 13 months ago by James W. MacDonald48k
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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$genes if yes then is there a way to keep both? ...
written 13 months ago by mictadlo0
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How to filter glmTreat results by a false discovery rate (FDR) of 0.05
... Hello, Currenty, I call glmTreat method as following: tr <- glmTreat(fit, contrast=B.LvsP, coef = 2, lfc=log2(1.5)) topTags(tr) I discovered this paper and In the "Differential gene and microRNA expression" section they described that the differentially expressed genes (DEGs) were filtered us ...
edger written 13 months ago by mictadlo0 • updated 13 months ago by Aaron Lun21k
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adding a description column to glmTreat output
... Hi, Below is my current code: y <- DGEList(counts=rawCountTable, group=group, genes = rownames(rawCountTable)) > head(y$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 13 months ago by mictadlo0 • updated 13 months ago by Aaron Lun21k

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