User: Paquet, Agnes

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Paquet, Agnes500
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Posts by Paquet, Agnes

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Answer: A: error message
... Hi Christina, It looks like you are trying to read in arrays with different print layout. What type of arrays are you using? Do they come from the same print? Best, Agnes ________________________________ From: bioconductor-bounces@stat.math.ethz.ch on behalf of Christina Tigress Sent: Thu 2/14/ ...
written 11.4 years ago by Paquet, Agnes500
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Answer: A: OntoCompare Error
... Dear Sebastien, Thank you very much for reporting this problem in ontoCompare. The affy id that you are using as example doesn't have any GO annotations (the associated value is NA), and this is causing the error. I will work on fixing this problem and commit a new version of the code as soon as p ...
written 11.7 years ago by Paquet, Agnes500
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Answer: A: Getting top level GO category for a list of genes
... Hi Palle, You can take a look at the package goTools. The main function ontoCompare takes lists of GO ids as argument (you will need to set the argument probeType="GO" in the function) and returns the number GO ids below top GO nodes. The default nodes are 1 step below MF, BP and CC, but you can m ...
written 11.9 years ago by Paquet, Agnes500
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Answer: A: ontoCompare - 1) notFound 2) GO level
... Hi Michaela, You can generate a different endnode list using the function CustomEndNodeList: MFendnode <- CustomEndNodeList("GO:0003674", rank=3) ontoCompare(affylist, probeType="hgu133a", endnode=MFendnode, goType="MF") You can also select endnodes of interest for your project using a GEO bro ...
written 11.9 years ago by Paquet, Agnes500
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Answer: A: goTools: ontoCompare - GO list
... Hi Christelle, ontoCompare provides several methods for counting the number of GO ids children to a top node. In your case, you can use the TIDS method, which returns the number of children of each node / total number of GO ids describing the group of proteins you provide in input. You can use t ...
written 11.9 years ago by Paquet, Agnes500
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Answer: A: Error with arrayQuality
... Hi Shripad, What kind of arrays are you working with? arrayQuality provides different functions for different types of arrays, and you will need to use the one that matches the arrays your are analyzing. gpQuality is expecting two-color microarray in the .gpr file format from GenePix, and agQuality ...
written 12.0 years ago by Paquet, Agnes500
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Answer: A: Problem with ArrayQuality Package version 1.12
... Thank you very much for the examples Martin, Agnes -----Original Message----- From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: Fri 7/6/2007 1:37 PM To: Paquet, Agnes Cc: pwhite at mail.med.upenn.edu; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Problem with ArrayQuality Package ve ...
written 12.0 years ago by Paquet, Agnes500
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Answer: A: Problem with ArrayQuality Package version 1.12
... Hi Peter, I just remembered now that we have added a namespace file for arrayQuality in the new release, and the function you are trying to use is not exported anymore. I need to do some check to see if exporting these function would conflit with anything else before I can change the file, so the e ...
written 12.0 years ago by Paquet, Agnes500
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Answer: A: Problem with ArrayQuality Package version 1.12
... Hi Peter, I just tried to run the function meeboQuality, which calls gpFlagWt, with the same R and BioC setting as you and it worked fine. Could you please email me the R code you are trying to run so that I can reproduce the error? Thank you very much, Agnes ________________________________ Fro ...
written 12.0 years ago by Paquet, Agnes500
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Answer: A: goTools: ontoCompare question
... Hi Dave, The current algorithm in ontoCompare is the following: - for each probe id in your list, retrieve all GO ids corresponding to this probe id - then, map these Go ids up to the end nodes provided as argument to the function (or the default ones) - Once the mapping is finished, add 1 to the ...
written 12.1 years ago by Paquet, Agnes500

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