User: January Weiner

gravatar for January Weiner
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Posts by January Weiner

<prev • 26 results • page 1 of 3 • next >
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Answer: A: Installing ShortRead - error: zlib not found even with zlib in LD_LIBRARY_PATH
... It is sufficient to set the compilers `-L` flag to point to the conda's library. If you downloaded the ShortRead package to, say, `ShortRead_1.38.0.tar.gz`, your conda environment is called `myconda` and your conda installation is in `/your/conda/directory/`, then it is sufficient to run conda ...
written 3 months ago by January Weiner240
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Comment: C: Effect size similar to Cohen's d in limma
... Thanks, I'll go with that. ...
written 4.0 years ago by January Weiner240
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Comment: C: Effect size similar to Cohen's d in limma
... Thanks, I'll go with that. ...
written 4.0 years ago by January Weiner240
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Comment: C: Effect size similar to Cohen's d in limma
... Thanks. I have seen this question. However, I am looking for a standardized effect size -- one that takes into account the variability. For example, a log fold change of 4 with CI ranging from 0.5 to 8 has a lower standardized effect size than a log fold change of 3 with CI from 2.5 to 3.5.  ...
written 4.1 years ago by January Weiner240
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Effect size similar to Cohen's d in limma
... What is the recommended way of calculating a standardized effect size for each gene in limma, preferably based on the fit object returned by lmFit? Possibly, would that be something like f$coefficients / f$stdev.unscaled ...
limma effect size written 4.1 years ago by January Weiner240 • updated 4.1 years ago by Ryan C. Thompson7.4k
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Comment: C: Standard error and effect size from Limma
... I am confused; shouldn't that be sqrt(fit$s2.post)? Similar to the line 255 of the toptable.R file in limma source package, the confidence intervals are calculated using  sqrt(eb$s2.post[top])*fit$stdev.unscaled[top,coef]*qt(alpha,df=eb$df.total[top]) ...
written 4.1 years ago by January Weiner240
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Gene shaving for bioconductor?
... Is there a package for gene shaving (Hastie 200: http://genomebiology.com/2000/1/2/research/0003) for Bioconductor? If not, is there interest in such a package? Kind regards, January -- -------- January Weiner -------------------------------------- [[alternative HTML version deleted]] ...
written 5.8 years ago by January Weiner240 • updated 5.8 years ago by Kevin Coombes430
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Comment: C: Analysing Affy data with limma
... Hi James, yes, we do see a similar response in other data sets (with more samples) that we and others have generated, but it still feels a bit weird. I have omitted the question of pairing for the sake of the simplicity here, but I agree that I need to include this in the calculations. I use dupli ...
written 5.8 years ago by January Weiner240
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Analysing Affy data with limma
... Dear all, I'm trying to analyse a data set reposited in GEO. In theory, I could download the CEL files and do everything from scratch, but I would prefer to use the GEO-reposited, normalized data. I load the data with library( GEOquery ) g <- getGEO( "GSE31348" )[[1]] So far, so good. The dat ...
limma geoquery written 5.8 years ago by January Weiner240 • updated 5.8 years ago by James W. MacDonald51k
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Differential gene expression of a cluster or group of genes
... Hello, this sounds like a rather trivial question but somehow the an answer eludes me. I am analysing gene expression data with limma in a two-factor model with interactions. No problems there. What I would like to do is to first cluster the genes (using my own clustering procedure that I'm workin ...
go limma written 5.9 years ago by January Weiner240 • updated 5.9 years ago by Gordon Smyth38k

Latest awards to January Weiner

Popular Question 4.0 years ago, created a question with more than 1,000 views. For Effect size similar to Cohen's d in limma
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Cell-type enrichment for gene expression
Popular Question 4.0 years ago, created a question with more than 1,000 views. For GSEA for R

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