User: Tim Rayner

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Tim Rayner270
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Posts by Tim Rayner

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Comment: C: Help on experiment design
... Dear Mike, Thanks for your email, and thanks to Marc for stepping in so promptly. Marc's analysis is quite correct - the makeChrStrandData function needs the row names of your data matrix to correspond to the probe or gene identifiers used by the annotation library package. In the case of org.Mm.eg ...
written 8.9 years ago by Tim Rayner270
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crlmm and snpMatrix
... Hi, I'm not sure if this really qualifies as a bug, but I've spent the morning tracking down an odd interaction between the crlmm and snpMatrix packages and I thought I should share it and maybe save others some time. It looks as though an object in the snpMatrix namespace is clobbering something n ...
snpmatrix crlmm written 9.1 years ago by Tim Rayner270 • updated 9.1 years ago by Benilton Carvalho4.3k
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Comment: C: BayesPeak segfault woes
... Hi Jonathan, Thanks very much indeed - the new BayesPeak version does seem to fix the segfault issue. Best regards, Tim On 4 June 2010 15:26, Jonathan Cairns wrote: > Hi Tim, > > I was able to analyse the .bed file you linked to (I assume there is no > associated control file?) wit ...
written 9.1 years ago by Tim Rayner270
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Comment: C: BayesPeak segfault woes
... Hi Jonathan, Thanks for the speedy reply. I tried running bayespeak on this file several times, and each time I got a segfault at roughly the same spot: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM315nnn/GS M315954/GSM315954_memory%2DCD8%2Dnaive%2DH3K4me3.bed.gz I'm not sure if i ...
written 9.1 years ago by Tim Rayner270
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BayesPeak segfault woes
... Hi, I'm trying to run the bayespeak function on some BED files published by Araki et al. (PMID 19523850, GEO accession GSE12616), and I'm having segfault problems which seem to relate to memory usage. I originally tried running the function on the whole BED files but that ran into problems very qui ...
bayespeak written 9.1 years ago by Tim Rayner270 • updated 9.1 years ago by Jonathan Cairns130
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Comment: C: getGEO - getting the .CEL files from GEO
... On 17 March 2010 16:51, Sean Davis wrote: > 2010/3/17 Vincent Carey : >> do you really want to put sample-characteristics data in a CEL file? >> >> the sample characteristics are available as follows: >> >> ?ff = getGEO("GSE4045") >> >>> table(pData(f ...
written 9.3 years ago by Tim Rayner270
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vsn and oligo (or xps?) packages for GeneST expression arrays
... Hi, I'm curious to know whether there are any plans to support the use of the VSN algorithm (i.e. the vsn package) with the classes defined by the oligo package. The reason I ask is that it seems as though the latter package is now touted as one of the supported methods of handling Affymetrix GeneS ...
vsn oligo xps written 9.5 years ago by Tim Rayner270 • updated 9.5 years ago by cstrato3.9k
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Answer: A: Genotype imputation
... Hi Antoni, I've been using the snpMatrix package for imputing SNPs which are not present on our platform. There's a convenient package vignette to walk you through the procedure. I've not tried imputing missing values, so I can't comment on that. Regards, Tim Rayner -- Bioinformatician Smith Lab ...
written 9.7 years ago by Tim Rayner270
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Comment: C: regarding package ArrayExpress
... Hi, This would work assuming the featureData is kept synchronised with the assayData. I guess the alternative would be to take mean or median for the duplicated reporters, which might be more useful in some cases. Perhaps that could be added as an option? I know quite a few custom-printed arrays ha ...
written 9.9 years ago by Tim Rayner270
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Comment: C: regarding web interface to R coding
... Another possibility is Biocep-R, which is more Java-based than strictly web-based, although such distinctions are now blurring: http://biocep-distrib.r-forge.r-project.org/ I've not tried using it for anything serious yet, but it might fit your purposes if you want distributed access to a central ...
written 9.9 years ago by Tim Rayner270

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