User: tkapell

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tkapell0
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Posts by tkapell

<prev • 29 results • page 1 of 3 • next >
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Is DESeq2 normalisation method appropriate for datasets with multiple cell types?
... Hi all, a theoretical question about DESeq2. I have a dataset of sorted blood immune cell types from healthy and diseased humans. I want to calculate DE genes for all the immune cell types so that I can generate a pan-immune disease signature. My worry is that since the blood immune cell types ...
normalization deseq2 written 27 minutes ago by tkapell0
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Comment: C: Error in sva() function: missing values, NaNs produced
... Yes, *Sequencing.lane* refers to different dates so they were really put on separate flow cells. ...
written 12 days ago by tkapell0
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Comment: C: Error in sva() function: missing values, NaNs produced
... I see. The only explanation I can think is that the batch that causes the problem is *Age*. There are a few patients that have the same value. Is it possible to remove this unwanted variation from my model? ...
written 12 days ago by tkapell0
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Comment: C: Error in sva() function: missing values, NaNs produced
... min(ncol(dat), nrow(dat)) - ceiling(sum(hat(mod))) [1]1 ...
written 12 days ago by tkapell0
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Comment: C: Error in sva() function: missing values, NaNs produced
... Thanks James, I followed your advice and used the *svaseq()* function instead. This time I had a different error: dat<-counts(dds,normalized=T) idx <- rowMeans(dat) > 1 dat <- dat[idx,] mod<-model.matrix(~ Age+Sequencing.lane+Disease, colData(dds)) mod0< ...
written 12 days ago by tkapell0
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Error in sva() function: missing values, NaNs produced
... Hi, I want to clean my RNA-seq data with the SVA package, but the *sva()* function gives me error: ``` *Error in density.default(x, adjust = adj) : 'x' contains missing values In addition: Warning message: In pf(fstats, df1 = (df1 - df0), df2 = (n - df1)) : NaNs produced* ``` I attach the code I ...
sva batch-correction written 13 days ago by tkapell0 • updated 13 days ago by James W. MacDonald51k
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Comment: C: Cannot install Bioconductor v3.9
... Thank you for the prompt answer ...
written 6 weeks ago by tkapell0
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Cannot install Bioconductor v3.9
... Hi all, I am trying to update a Bioconductor package (*scran*) which is a dependency for another one (*cellassign*) and so I had to update my Bioconductor version from 3.7 to 3.9 (I am using R 3.6.1). I got the following message and nothing was updated. Can somebody provide a quick fix? Thanks ...
bioconductor scran cellassign written 6 weeks ago by tkapell0 • updated 6 weeks ago by Martin Morgan ♦♦ 24k
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Installation of r2excel package
... Hi, I m trying to install r2excel from the kassambara github, but I get the following error. Can anyone help? Installing package into ‘C:/Users/Theo/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) * installing *source* package 'r2excel' ... ** R ** byte-compile and prepa ...
packages github written 10 months ago by tkapell0 • updated 10 months ago by Gordon Smyth39k
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Comment: C: DESeq2: removal of duplicated genes during statistical analysis
... I did a gene differential expression analysis using transcriptome levels therefore my count table has transcript version IDs (e.g. ENSG00000000003.14). When I convert those to ensembl IDs (e.g. ENSG00000000003), there are about 30 genes which share the same ensembl ID because they are paralogs in th ...
written 11 months ago by tkapell0

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