User: Leif Väremo

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Leif Väremo70
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Posts by Leif Väremo

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Comment: C: How to handle mix of samples from the same subject and from different subjects d
... Ah, yes of course! For reference, I tried both alternatives (single and double voom) and the results (adjusted p-values of the coefficients) are very consistent (Pearson correlation >0.99). ...
written 3.8 years ago by Leif Väremo70
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Comment: C: How to handle mix of samples from the same subject and from different subjects d
... Thanks for your fast suggestion! I had totally missed this section in the limma guide. I have run voom only once, since the attempt to run a second pass after the duplicateCorrelation returned an error: Error in lowess(sx, sy, f = span) : 'delta' must be finite and > 0 In addition: Warning mes ...
written 3.8 years ago by Leif Väremo70
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How to handle mix of samples from the same subject and from different subjects during differential expression analysis of RNA-seq using GLMs?
... Hi, I am performing differential expression analysis of RNA-seq data using GLMs in edgeR. I have an experimental design with 4 different groups of subjects in a 2k-factorial design (6 different subjects per group). In other words, a control group, a group with condition A, a group with condition B, ...
rnaseq edger differential expression differential gene expression rna-seq written 3.8 years ago by Leif Väremo70 • updated 3.8 years ago by Ryan C. Thompson7.4k
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Running the GSEA algorithm
... Isn't the existing GeneSetEnrichment biocView sufficient? It's nested under Software>Bioinformatics>Enrichment in release and Software>BiologicalQuestion> in devel. All the best Leif On Mon, Mar 31, 2014 at 11:01 PM, Ryan wrote: > Yes, I think that would be helpful. There are a * ...
microarray genesetenrichment pgsea gseabase gsri seqgsea written 5.5 years ago by Leif Väremo70 • updated 5.5 years ago by Steve Lianoglou12k
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Comment: C: pre-ranked GSEA within R?
... Dear Pekka and Daniel, Yes, the GSEA implementation in piano is one of the slowest (of the implemented methods), however since version 1.2.0 the argument ncpus was added and let's you run the algorithm on multiple cpus (using the R package snowfall) thus decreasing the runtime (especially if you ha ...
written 5.7 years ago by Leif Väremo70
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Comment: C: relations package
... Hi, I think you can still install it from source: install.packages("relations",type="source") Hope that helps! Leif On Wed, Aug 21, 2013 at 5:31 PM, Dan Tenenbaum wrote: > On Wed, Aug 21, 2013 at 4:21 AM, Nikul Soni > wrote: > > installing some packages required some dependencie ...
written 6.2 years ago by Leif Väremo70
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Different colors in vennDiagram?
... Hi, I am trying to use the vennDiagram function of the limma package to color the circle borders in different colors. This works fine for up to three circles, but for four and five circles I can not get it to work. Does anyone have a solution for this? Below is some sample code to reproduce my iss ...
limma written 6.3 years ago by Leif Väremo70 • updated 5.0 years ago by Gordon Smyth38k
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Comment: C: lmFit not keeping rownames of arg object?
... Dear Gordon, An update to my previous mail. I did now try with the latest version of limma through svn (still version 3.17.3 though), built and installed, and the problem disappeared. Did you just not bump the version number so it did not get passed to the build system? My previous tries were on i ...
written 6.5 years ago by Leif Väremo70
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Comment: C: lmFit not keeping rownames of arg object?
... Dear Gordon, I removed and reinstalled limma, just to be sure. Here is my output when running your example in a "fresh" R session, still I have the problem when using the coef argument: > library(limma) > y <- matrix(rnorm(26*4),26,4) > rownames(y) <- letters[1:26] > design & ...
written 6.5 years ago by Leif Väremo70

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