User: ecg1g15

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ecg1g150
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Posts by ecg1g15

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Plot genes with similar expression patterns
... Thanks Michael, I have done many types of clustering using vsd. But more than doing a hierarchical clustering, I mean to plot the actual expression profiles (y-axis) over time/geography (x-axis), and then generate the cluster plots by profile similarity. (ie Cluster 1: gene expression gradual incre ...
written 5 days ago by ecg1g150
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Comment: C: Plot genes with similar expression patterns
... Thanks Michael, I have done many types of clustering using vsd. But more than doing a hierarchical clustering, I mean to plot the actual expression profiles (y-axis) over time/geography (x-axis), and then generate the cluster plots by profile similarity. (ie Cluster 1: gene expression gradual incre ...
written 5 days ago by ecg1g150
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Plot genes with similar expression patterns
... Hi, I have been using the "Analyzing RNA-seq data with DESeq2" (Love, Anders and Huber) and worked really well so far, thanks guys! However, I would like to export and plot the different **expression patterns** of genes within my dataset. What I mean is to be able to group them by similar express ...
rnaseq deseq2 R written 6 days ago by ecg1g150 • updated 5 days ago by Michael Love23k
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Answer: A: Change order of conditions when plotting: plotCounts {DESeq2}
... I have found that you can manually change the order like this: ddsMat$location <- factor(ddsMat$location, levels=c("West", "Mid", "East")) ...
written 11 days ago by ecg1g150
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Answer: A: Change order of conditions when plotting: plotCounts {DESeq2}
... I have found that you can manually change the order like this: ddsMat$location <- factor(ddsMat$location, levels=c("West", "Mid", "East")) ...
written 11 days ago by ecg1g150
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Change order of conditions when plotting: plotCounts {DESeq2}
... I have a df of 17 variables (my samples) with the condition location which I would like to plot based on a single gene "gene1" When plotting: library(DeSeq2) plotCounts(df, "genename", intgroup=c("location")) By default, the function plots the "conditions" alphabetically on the graph eg: E ...
deseq2 R plotcounts written 11 days ago by ecg1g150
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Comment: C: DESeq2: differential expression analysis from matrix count with gene annotation
... > ddsMat <- DESeqDataSetFromMatrix(countData = table_samples, + colData = colData, + design = ~ location) Error in DESeqDataSetFromMatrix(countData = table_samples, colData = colData, : ncol(countData) == nrow(colData) is ...
written 29 days ago by ecg1g150
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Comment: C: DESeq2: differential expression analysis from matrix count with gene annotation
... Thanks Michael, ddsMat <- DESeqDataSetFromMatrix(countData = table_samples, + colData = colData, + design = ~ location) brings me this error: Error in DESeqDataSetFromMatrix(countData = table_samples, colData = ...
written 29 days ago by ecg1g150
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DESeq2: differential expression analysis from matrix count with gene annotation
... I am trying to analyse my transcript data to generate heat maps, PCAs and see the differential expression between samples. I don't necessarily need the coldata, as I already know the conditions for each sample name but if so, it would be location, West, Mid and East. sample location X1473 M ...
deseq2 dataframe pasilla written 29 days ago by ecg1g150 • updated 29 days ago by Michael Love23k
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Comment: C: caught segfault error when loading S4Vectors package in R
... Hi @Martin, I ended up fixing this I believe! (now I have different errors but nothing to do with this!) So, yes you are right, I have used two different ways of installing packages (CRAN on R, and bioconductors on shell terminal), the problem comes when it's trying to load the DESeq2 package, an ...
written 11 weeks ago by ecg1g150

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