User: CodeAway

CodeAway20
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Posts by CodeAway

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Comment: C: Input genes for GSVA
... Thank you Robert!  I appreciate your response.     ...
written 8 weeks ago by CodeAway20
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... Hello All, I would like to know what exactly should be the set of genes that go as input in the expression matrix to GSVA (not the gene set but the expression matrix). I am working particularly within the context of single-cell data, and have marker genes for two groups. I would like to find out th ...
written 9 weeks ago by CodeAway20 • updated 8 weeks ago by Robert Castelo2.2k
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... I solved this myself as follows: ttxx <- colorRampPalette(brewer.pal(12,"Paired"))(length(levels(top20mrks$cluster))) names(ttxx) <- levels(top20mrks$cluster) ha_row <- HeatmapAnnotation(df = data.frame(Cluster=top20mrks$cluster), which="row", col = list(Cluster = ttxx)) Now it works. ... written 9 months ago by CodeAway20 0 answers 301 views 0 answers ... Further to my post above, I tried doing this: ha_row <- HeatmapAnnotation(df = data.frame(Cluster=top20mrks$cluster), which="row", col = list(Cluster = colorRampPalette(brewer.pal(12,"Paired"))(length(levels(top20mrks\$cluster)))) ) But I got the following error: E ...
written 9 months ago by CodeAway20
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... Hello All, I love the ComplexHeatmap package, and have been using it to make some gene expression heatmaps.  If I wish to add row annotations for genes, with each gene belonging to one of 10 clusters, how do I make automatic color assignments to the groups instead of giving them as a list manually? ...
written 9 months ago by CodeAway20
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... Thanks, Michael.  Yes, that makes it clear.  So, in short, for regular bulk RNAseq data, would you recommend using the shrunken LFCs vs not using it?  As far as I understand, the main reason you decided to change the default in DESeq2, is for types of data other than bulk RNAseq, correct?  Thanks a ...
written 13 months ago by CodeAway20
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... Thank you very much, Michael, for the clarification, as I was looking for this answer and was getting confused about the removal of the  shrinkage feature by default from DESeq2.  So, would you say that for regular bulk RNAseq, we should use this shrinkage feature by default as usual like in the ol ...
written 13 months ago by CodeAway20
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... Thanks, James.  I am actually not using "size_by", so that is left to default. I was able to change the colors of the points as below: ppcah <- plotPCA(sce, pca_data_input="pdata", colour_by="sample_type", shape_by=NULL) +   scale_fill_manual(values=c("WT"="blue", "R172K"="red")) +   labs(fil ...
written 13 months ago by CodeAway20
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... Hello All, Just need a quick help, with regards to the plotPCA function of the "really excellent" scater package, that I am using for single-cell RNAseq analysis of 10X data.  I wish to change the size of the points and also remove the gray outlines that currently appear around the points. I tried ...
written 13 months ago by CodeAway20 • updated 9 weeks ago by angela.ubn0

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