User: Tim Yates

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Tim Yates250
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Posts by Tim Yates

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Comment: C: Class for a DataFrame of Matrices
... Good idea! Quick question though, is it possible to handle rectangular objects as cells (rather than columns)? So I end up with: DataFrame with 2 rows and 2 columns a b 1 M1 M3 2 M2 M4 Where M1-4 are Matrix objects? Cheers, Tim PS: Originall ...
written 6.4 years ago by Tim Yates250
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Class for a DataFrame of Matrices
... Hi all! Is there a class that will allow me to have a Table (or DataFrame) of sparse Matrices? data.frame and DataFrame don't work even if I wrap the Matrix like so DataFrame( I( Matrix( nrow=10, ncol=10, sparse=T ) ) ) with the latter So does something exist that I can use? Just thought I'd ...
written 6.4 years ago by Tim Yates250 • updated 6.4 years ago by Michael Lawrence11k
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Answer: A: annmap installation window
... Hi Chris, This sounds like a problem with the RMySQL installation on your machine. Can you verify it works before trying to install annmap? Unfortunately, we don't have a Windows machine with enough horsepower to build, run or test annmap on the Windows platform, and that (and that I had some prob ...
written 6.4 years ago by Tim Yates250
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Answer: A: problems with Affymetrix probes id using exonmap and xmapcore
... Hi again Sorry for the late responses, it's a big public holiday here in the UK... Can you give an example of the code which is returning NULL? Cheers, Tim On 28/04/2011 16:05, "Gomez Moruno, Antonio" wrote: > Hi Tim, > > the problem is that i need to process the data previously wit ...
written 8.1 years ago by Tim Yates250
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problems with Affymetrix probes id using exonmap and xmapcore
... Sorry, my phone decided to send this response off list... --- Hiya, You seem to have both the deprecated exonmap package, and the xmapcore package loaded at the same time. This will cause misbehavior at best, and crashes at worst. Can you try with just xmapcore loaded, and if that still doesn't ...
annotation cdf exonmap xmapcore written 8.1 years ago by Tim Yates250
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Comment: C: xmapcore
... I realised last night on my way home that there was a slight issue with this code for the reverse strand transcripts. This version should fix that. (I have updated the code on the github gist link as well -- I'm just posting it here in case someone finds this email in a future search) transcript. ...
written 8.3 years ago by Tim Yates250
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Comment: C: xmapcore
... Hi again Brian, Sorry for the delay in replying, I wanted to make sure I got this code right (I think it's right now) ;-) -- Just in case the email gets the code garbled, I've also pasted it here: https://gist.github.com/89d35075b969af50a3f9 transcript.to.translatedprobes = function( transcript.id ...
written 8.3 years ago by Tim Yates250
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Answer: A: xmapcore
... Hiya! It depends what sort of output format you want for your data. For example, say you are interested in 'ENST00000413465' (a transcript of TP53) http://bit.ly/e9rSMg You could do the following: > probe.rd = xmap.range.apply( transcript.details( 'ENST00000413465' ), function( ch, s, e, st ...
written 8.3 years ago by Tim Yates250
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Comment: C: what's really in hgu133plus2.db?
... Hi Michal :) Yeah, the HGU133plus2 array went in to the xmapcore database as of version 58, and the HuGene-1_0-st-v1 (Human Gene 1.0 ST Array plus 2) went in at version 60 (the current latest version) In the xmapcore package, the method to set the current array you are using is xmap.array.type(). ...
written 8.3 years ago by Tim Yates250
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Answer: A: what's really in hgu133plus2.db?
... We map the hgu133plus2 array to ensembl as part of the xmapcore package. The mappings can be seen on the xmap browser http://xmap.picr.man.ac.uk/?a=HG-U133Plus2&ch=17&lay=gene&q=Tp53 Our you can install the human xmapcore database (from the downloads page of that site) into a local c ...
written 8.3 years ago by Tim Yates250

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