User: James Perkins

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James Perkins120
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Posts by James Perkins

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Measuring shifts in intronic expression independently of exons
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written 5.7 years ago by James Perkins120 • updated 5.7 years ago by Wolfgang Huber13k
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return value used for filter amongst attributes, getBM(), biomaRt
... Dear list, Is there a way to keep track of the values used for the filter when using the getBM() function from the biomaRt package? I have some genomic regions and want to find out what genes are in these regions. This is simple enough using getBM(): require(biomaRt) ensembl = useMart("ensembl", ...
go biomart genomicranges written 5.9 years ago by James Perkins120
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Answer: A: ReadqPCR: [[hkgs,]] incorrect number of dimensions
... Hi Franklin, It looks like the problem is due to you only having 1 replicate for case and 1 for control, and so it can't work out stats etc. I will work on a fix for this, in the meantime you can work out delta delta Cq by subracting 1 column from qPCRBatch.dcq from the other (followed by 2^ tranfo ...
written 6.1 years ago by James Perkins120
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workflow from NormqPCR 5.1 to 5.3
... Hi Franklin, Replies below, On 28 February 2013 20:36, Franklin Johnson [guest] wrote: > > Dear Maintainer, > > I have created my.qPCRBatch object read into R using the ReadqPCR package: > > rownames(exprs(qPCRBatch)) > [1] "actin_14d_TechReps.1" "actin_14d_TechReps.2" "act ...
qpcr normqpcr written 6.2 years ago by James Perkins120
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Oligo - oligo::probeNames() returns transcript clusters, not probe sets
... Hi all, I've just noticed a possible bug in oligo. When using oligo::probeNames to return the probeset mappings for the probes in the unprocessed GeneFeatureSet, in older versions we obtain the probeset ids However in R-2.15.1 (and also in the latest version of R, though not shown) we appear to be ...
probe oligo written 6.2 years ago by James Perkins120 • updated 6.2 years ago by James W. MacDonald49k
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Comment: C: RNA-seq, low count filtering and multiple testing
... Hi Ryan, Michael, Gordon Thanks Ryan, your less directed filter of lowly expressed genes makes sense to me, I guess there could be some genes taht get through such as for example: control1 control2 control3 case1 case2 case3 geneB 20 10 0 1 0 ...
written 6.4 years ago by James Perkins120
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RNA-seq, low count filtering and multiple testing
... Hi all, I understand it is normal to filter out lowly expressed genes before performing differential expression analysis on RNA-seq data (e.g., edgeR, DESeq). However I notice with such methods as edgeR, I find a number of genes where there is clearly one outlier that is causing the gene to be dee ...
edger written 6.4 years ago by James Perkins120 • updated 6.4 years ago by Gordon Smyth37k
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Comment: C: Oligo package, possible bug in paCalls
... Thanks for the speedy fix! I downloaded from svn and so far it seems to be working ok. Cheers, Jim On 4 July 2012 17:49, Benilton Carvalho wrote: > this has been addressed on oligo 1.20.4, which should appear online soon. b > > On 4 July 2012 12:01, Benilton Carvalho > wrote: > ...
written 6.8 years ago by James Perkins120
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Oligo package, possible bug in paCalls
... Dear Benilton, I had a problem running paCalls() from the oligo package, specifically I got: Error in dimnames(res) <- list(fid, sampleNames(x)) : length of 'dimnames' [1] not equal to array extent > if (require(oligoData) & require(pd.huex.1.0.st.v2)){ + data(affyExonFS) ...
oligo written 6.8 years ago by James Perkins120 • updated 6.8 years ago by Benilton Carvalho4.3k
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Ensembl gene ids corresponding to affymetrix rat exon array transcript level ids
... Hey, Has anyone ever used biomart to get the ENSEMBL ids for the Affymetrix rat exon array at the transcript cluster level: i.e. library(oligo) exonCELs <- list.celfiles("where the rat CEL files are", full.names=TRUE) affyExonFS <- read.celfiles(exonCELs) exonCore <- rma(affyExonFS, targ ...
biomart oligo written 7.1 years ago by James Perkins120

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Popular Question 5.7 years ago, created a question with more than 1,000 views. For RNA-seq, low count filtering and multiple testing

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