User: ecg1g15

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ecg1g150
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Posts by ecg1g15

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RNASeq biplot variables and samples
... I would like to generate a biplot I have been following the Love et al (2019) version of RNASeq analysis using DESeq, and have been able to plot PCAs, however, they haven't designed a function of generating billets yet http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.h ...
rnaseq deseq2 written 5 hours ago by ecg1g150
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Answer: A: Reordering clusters when plotting pheatmap in R
... I have found you can use clustering_callback function, but I need to construct it, how do I do it? > clustering_callback callback function to modify the clustering. Is > called with two parameters: original hclust object and the matrix used > for clustering. Must return a hclust object. ...
written 20 days ago by ecg1g150
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Reordering clusters when plotting pheatmap in R
... I am plotting a set of genes belonging to three groups A, B, C, and the heatmap orders them such as C, A, B. (I have read this is due to that it plots on the right the cluster with the strongest similarity). I would like to order the clusters to the groups are seen as A, B, C (therefore reorganising ...
R clusters pheatmap written 20 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 9 weeks 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 9 weeks 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 9 weeks ago by ecg1g150 • updated 9 weeks ago by Michael Love24k
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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 9 weeks 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 9 weeks 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 10 weeks 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 12 weeks ago by ecg1g150

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