User: Perry Moerland

gravatar for Perry Moerland
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Bioinformatics Laboratory, Academic Medical Center, Amsterdam, the Netherlands
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2 months, 3 weeks ago
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13 years, 10 months ago
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Posts by Perry Moerland

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Moderated F-statistics for time course experiment
... Dear Gordon, I was already suspecting that voom was causing the observed differences. Thanks for confirming this and showing that everything is indeed as expected with limma-trend. What would your recommendation be when using the voom pipeline and having to choose between three 'equivalent' sets of ...
written 10 months ago by Perry Moerland110
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Moderated F-statistics for time course experiment
... Dear all, In an RNA-seq time course experiment I was analyzing I was expecting identical moderated F-statistics (calculated using topTable) for a set of contrasts where each timepoint is compared with baseline and the 'equivalent' set of contrasts where each timepoint is compared with the previous ...
rnaseq limma written 10 months ago by Perry Moerland110 • updated 10 months ago by Gordon Smyth35k
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Answer: A: Limma Voom produces many identical adjusted p-values
... Hi Benjamin, There is indeed a logical explanation for these runs of identical adjusted p-values when using the Benjamini-Hochberg (BH) method. To quote Wikipedia: "The Benjamini–Hochberg procedure (BH step-up procedure) controls the FDR at level alpha. It works as follows [for p-values in ascendi ...
written 11 months ago by Perry Moerland110
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Answer: A: EdgeR LogCpm and LogFC values calculation
... Dear Koen, The source code of the function aveLogCPM (included in the package source of the current release version 3.4.2) shows that the function mglmOneGroup needs some additional parameters and other default values than the ones you used: prior.count <- 2 dispersion <- 0.05 # y is the ...
written 4.9 years ago by Perry Moerland110
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inconsistency in illuminaHumanv4.db?
... Hi Mark, Thanks for your detailed reply! Are you planning to persuade them to rerun the Perl script with the last version of UniGene for the next release of the illuminaHumanv4.db package (and the other Illunmina re- annotation packages)? best, Perry --- Perry Moerland, PhD Room J1B-215 Bioinformat ...
annotation written 5.0 years ago by Perry Moerland110
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inconsistency in illuminaHumanv4.db?
... Dear all, dear Mark, I'm a grateful user of the illuminaHumanv4.db annotation package. One of my collaborators is interested in probes mapping to C1orf151 according to the reannotation provided by the package. However, the re-annotation for these probes seems inconsistent: > Illids = get("C1orf ...
annotation written 5.1 years ago by Perry Moerland110 • updated 5.1 years ago by Mark Dunning1.1k
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Comment: C: Limma Multi-level Experiments
... Dear Michael, This is a perfectly valid approach and has been described by Gordon in section 3.5 'Comparisons Both Between and Within Subjects' of the edgeR manual. Note however that baseline differences at time A between diseased and normal cannot be estimated with this design matrix. This can be ...
written 5.4 years ago by Perry Moerland110
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Comment: C: inSilicoMerging and Limma
... Dear Ed, This behaviour is indeed expected when you merge datasets as you did. The two datasets are completely confounded with your contrast of interest: Hsu corresponds to the EXP condition and Kai to the CTL condition. Using ComBat to merge the two datasets, you actually took care that the mean e ...
written 5.5 years ago by Perry Moerland110
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Answer: A: Problem with Beadarray package for beadchipHT-12
... Hi Leon, Could you tell us where your code stops working, include the error message, and also include a sessionInfo(), otherwise it will be hard to give you any input. best Perry Leo Nitsche wrote: > Hi all, > > > I have already obtained a data set from Illumina Beadchip-HT12 experience ...
written 9.4 years ago by Perry Moerland110
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Answer: A: Annotation.db: how automatically call a mapping?
... Dear Guido, A few weeks back I was struggling with the same problem and came up with this solution: makeMapping <- function(annotPkg,str="SYMBOL",ids){ do.call(library,list(annotPkg)) annotPkg = sub(".db","",annotPkg) f = function(x) mget(ids,x,ifnotfound=NA) an ...
written 9.5 years ago by Perry Moerland110

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Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Limma Voom produces many identical adjusted p-values

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