User: lemerle@embl.de

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Posts by lemerle@embl.de

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Answer: A: annotation package for ecoli2
... hi yanqin, you need to make your own, unless someone who's made one is willing to make it available. i sent the same email around a few months ago on this list with no success. if you feel up to it, check the annbuilder package, i was told that was a good place to start for making one yourself. i di ...
written 13.3 years ago by lemerle@embl.de50
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Comment: C: BH vs BY in p.adjust
... >> by the way, in cases that it's not uniformly distributed, from the >> range values >> of the over-represented bins on the histogram, can we not get an idea of the >> effect size associated with the differential probesets responsible for this >> non-uniformity ? >& ...
written 13.3 years ago by lemerle@embl.de50
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BH vs BY in p.adjust
... Quoting Wolfgang Huber : > Hi Caroline, > > what does > > hist(fit2$p.value[,1], breaks=100, col="orange") > > look like? hi wolfgang, well.... not at all uniform: > x <- hist(fit2$p.value[,1], breaks=30, > col="orange",main="distribution of raw p-values",labels=T) ...
coverage limma safe written 13.3 years ago by lemerle@embl.de50 • updated 13.3 years ago by Wolfgang Huber13k
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BH vs BY in p.adjust + FDR interpretation
... dear list, i am analysing a set of affymetrix chips using limma to get lists of differentially expressed probesets. concerning BH and BY, the two methods available with p.adjust that adjust p-values controlling for the false discovery rate, i was surprised to find a large discrepancy in the number ...
coverage limma written 13.3 years ago by lemerle@embl.de50 • updated 3.8 years ago by Gordon Smyth39k
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Affychip coli asv2 annotation files
... Dear list, I am analysing Affymetrix GeneChips of type coli asv2. I wanted to use the "annotate" package but found no appropriate annotation files in the bioc repository. I then found out about AnnBuilder, but the vignette mentions that for any species that are neither human, rat or mouse, AnnBuild ...
annotation annbuilder written 13.6 years ago by lemerle@embl.de50 • updated 13.6 years ago by Seth Falcon7.4k

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