User: Richard Pearson

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Posts by Richard Pearson

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Structural variations analysis
... Hi Vincenzo Apologies for the very delayed response! There is a function named vcf2sm in package GGtools that might help. I don't have any direct experience with this but thought I'd flag it up. Best wishes Richard On 23/03/2011 16:14, Vincenzo Capece wrote: > Dear all, > i am a beginner. ...
snp ggtools written 8.6 years ago by Richard Pearson160 • updated 8.6 years ago by Vincent J. Carey, Jr.6.3k
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Comment: C: *** caught segfault *** ....cause 'invalid permissions' with PUMA pachage
... Hi Alberto I have just run this same command, also on 64 bit ubuntu, with no problems. I think you didn't paste the full output of sessionInfo() - e.g. there are no attached packages shown. You do have version 2.2.0 of puma, right? Here's my full sessionInfo: > sessionInfo() R version 2.12.0 ...
written 9.1 years ago by Richard Pearson160
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Comment: C: Puma question
... Dear Marco Sorry, I have should have spotted this before. MoGene is an ST (exon) array, right? These arrays have no mm probes, and mmgmos requires both pm and mm probes. As such you will not be able to use mmgmos with this dataset. Best wishes Richard On 21/10/2010 10:28, Manca Marco (PATH) wrot ...
written 9.1 years ago by Richard Pearson160
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Answer: A: Puma question
... Hi Marco My guess is that there is a problem with your targets.csv file. It seems that your "adf" object has no varMetadata: varLabels and varMetadata description: X.Group.: X.Treatment.: To confirm this is not a problem specifically with puma, could you try a different summarisation ...
written 9.1 years ago by Richard Pearson160
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Answer: A: Subscripting GenomicRanges objects with [[ or $
... Hi Tim I think you need the values accessor method here: print( values(my.gr)[[ 'name' ]] ) Cheers Richard Tim Yates wrote: > Hi all, > > I'm trying to move to using GRanges objects for storing my genomic features > rather than IRanges objects that I use currently. > > Howeve ...
written 9.2 years ago by Richard Pearson160
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Comment: C: gc-rma and vsn normalization for rat microarray data
... Rainer Unfortunately you're not going to be able to use puma as the methods require both perfect match (PM) and mismatch (MM) data (and exon arrays have only the PM). Best wishes Richard Benilton Carvalho wrote: > Rainer, > > I understand I don't offer a vsn() method in oligo (yet), but ...
written 9.4 years ago by Richard Pearson160
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Answer: A: Fwd: microarray data without replication
... Hi Ina You've not said what microarrays you are using or what type(s) of analysis you want to do. If you're wanting to look for differentially expressed genes from Affymetrix arrays, both bgx and puma can make use of technical error from single arrays per condition. The bgx folks wrote a paper abou ...
written 9.5 years ago by Richard Pearson160
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Comment: C: Bioconductor Digest, Vol 87, Issue 10
... Hi Avinash So, it looks from your code like you haven't provided any phenotype information about your CEL files, and therefore each CEL file will be treated as a different condition. Because you have only 1 array per condition (i.e. you have no replicates), limma is going to give an error. Please n ...
written 9.5 years ago by Richard Pearson160
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Answer: A: Bioconductor Digest, Vol 87, Issue 10
... Avinash Please keep replies on list (reply to all). You've still not given a reproducible example - I don't know what your object eset_rma contains. Also, you've not provided the output of sessionInfo(). However, if eset_rma is the output of pumaComb, it will contain a single combined expression v ...
written 9.5 years ago by Richard Pearson160
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Comment: C: Bioconductor Digest, Vol 87, Issue 10
... Hi Avinash Please read the posting guide and provide a reproducible example and output of sessionInfo(). I'm guessing you don't have replicates of your conditions, and hence the error, but difficult to say without knowing exactly what you've done. Showing the output of pData() on your ExpressionSe ...
written 9.5 years ago by Richard Pearson160

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