User: Paul Geeleher

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Paul Geeleher1.3k
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Posts by Paul Geeleher

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Comment: C: RNA-seq differentially expressed gene finding methods
... Hi Son, My understanding is that the approach you describe could be considered valid for large enough numbers of samples, however, RNA-seq experiments will typically have smaller numbers (<30) samples per condition, meaning that a t-test is not valid (because RNA-seq data isn't normally distribu ...
written 3.2 years ago by Paul Geeleher1.3k
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Answer: A: Limma package and minimal number of genes
... Limma borrows information across all genes to better estimate variance for each gene, so your results should in theory be more accurate if you run the analysis for all genes on your arrays and export the p-values for the set of genes in which you are interested at the end of the analysis. Paul On ...
written 3.5 years ago by Paul Geeleher1.3k
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Answer: A: Gene expression and multivariables
... I could be missing something here but I don't think its super clear what you mean by "relate gene expression with multi variables". It might be helpful to elaborate a little. Paul. On Sun, May 25, 2014 at 9:46 AM, chris Jhon wrote: > Hi, > > > I have genome wide gene expression time ...
written 3.5 years ago by Paul Geeleher1.3k
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Answer: A: GWAS with family data
... GenABEL will allow you to do this fairly easily. Notably, it is also very well documented. EMMAX may provide something a little more cutting edge when analysing family GWAS (but not in an R environment): http://www.nature.com/ng/journal/v42/n4/abs/ng.548.html Paul. On Tue, Apr 15, 2014 at 12:09 P ...
written 3.6 years ago by Paul Geeleher1.3k
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Answer: A: recommend package for exon array analysis
... Check out in this paper: http://bib.oxfordjournals.org/content/12/6/634.long Paul. On Tue, Mar 18, 2014 at 3:21 PM, Dli [guest] wrote: > > Dear Community, > > I recently need to analysis batch of Mouse Exon ST 1.0 array, I have been tried to search existed packages for process this k ...
written 3.7 years ago by Paul Geeleher1.3k
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Answer: A: help with array based microRNA data analysis
... Here's a previous thread that may be relevant, although I'm not sure what you plan on doing without control samples... https://stat.ethz.ch/pipermail/bioconductor/2008-May/022460.html Paul. On Mon, Jan 20, 2014 at 12:05 PM, Abhishek Pratap wrote: > Hey Guys > > We have some custom array ...
written 3.8 years ago by Paul Geeleher1.3k
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Comment: C: scholarly reference for "don't draw PCA/heatmap dendrograms on DEGs"
... Hey Aaron, you can show this fairly easily with a couple of lines of code (using randomly generated data). I think Kevin suggested something like this too: library(genefilter) mat <- rnorm(100000) # generate a 10 x 10,000 matrix of random "gene expression" data dim(mat) <- c(10000, 10) myfac ...
written 4.0 years ago by Paul Geeleher1.3k
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Comment: C: Average expression value from limma
... Oh I may have misunderstood your question. There's no reason the average expression values (for any particular probe) should differ between limma or when you calculate them manually (assuming you aren't doing any additional normalization). You may have to provide code for somebody to be able to figu ...
written 4.5 years ago by Paul Geeleher1.3k
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Answer: A: Average expression value from limma
... Normally I think you'd expect that differentially expressed genes tend to have higher average intensity. Consider that your array is measuring approx 25,000 transcripts, this means that in your tissue type many of these will not even be expressed, thus are highly unlikely to be identified as differe ...
written 4.5 years ago by Paul Geeleher1.3k
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Comment: C: DESeq2 vs limma/voom: PCA completely different. How to proceed?
... Hey Stephen, A quick look suggests that your PC1 are actually very similar (look at only the X-axis on both of the PCA plots). My guess is that what was PC2 in one plot has become PC3 or PC4 etc. in the other plot. As you have only plotted PC1 and 2 the plots look completely different. Maybe try pl ...
written 4.6 years ago by Paul Geeleher1.3k

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Popular Question 3.2 years ago, created a question with more than 1,000 views. For rowttests() function in genefilter library
Popular Question 3.2 years ago, created a question with more than 1,000 views. For rowttests() function in genefilter library
Centurion 3.2 years ago, created 100 posts.

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