User: Paquet, Agnes

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Paquet, Agnes500
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Posts by Paquet, Agnes

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Answer: A: dye effects stronger than dye-swaps?
... Hi Jenny, There are a couple of other things you can check to make sure you have the correct orientation: - if this is a mutant vs. control, the investigator probably know about some upregulated/downregulated genes which caracterize the mutant. You can check the sign of the M values for probes corr ...
written 12.6 years ago by Paquet, Agnes500
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Problem with customised endnode list in ontoCompare(goToolspackage)
... Hi Manasa, The bug in CustomEndNodeList should be fixed in the new release version of goTools. There was a NA value in the list at rank=2 which caused the error, the new version will remove NAs automatically. For the 3 top nodes: these nodes are included by default to ensure that the loop in th ...
microarray go graph gotools category oligo written 12.6 years ago by Paquet, Agnes500
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marray and limma error with lmFit
... Dear Birger, I just tried the code from the book on R 2.4.0 and R 2.5.0 and I was not able to reproduce the error you are mentionning. My Bioconductor installation on R2.4.0 is the following: > sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1 ...
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Answer: A: maQualityPlots (arrayQuality package)
... Hi Joao, The fuction doesn't offer the capacity to easily change the number of replicates for your controls, but one way to fix this problem would be to overwrite the default function qpDotsPlot by the same function with a different value for the number of replicates. To do this, just load the pack ...
written 12.7 years ago by Paquet, Agnes500
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Answer: A: maQualityPlots (arrayQuality package)
... Dear Joao, This problem is most likely due to the format of your control spots. arrayQuality is looking for controls which are replicated more that 3 times on your array (more that 3 times the same oligo id). If you don't have such controls or if you didn't set up your controls properly in your RG ...
written 12.7 years ago by Paquet, Agnes500
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Answer: A: arrayQuality
... Hi Som, It is difficult to understand what is causing the error without more information on which version of R and arrayQuality you are using, and without knowing how you read the genepix data in. Could you please join the complete R code you used to read the data in (ie. how you created your data ...
written 12.8 years ago by Paquet, Agnes500
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Answer: A: OntoCompare Error
... Hi Johannes, Did you feed a list of GO ids or a vector? of GO ids? I took some of your ids to try to reproduce the error but I didn't get any. Here is what I did: mygo=c("GO:0003677", "GO:0004386", "GO:0005524", "GO:0016787", "GO:0001882", "GO:0003779", "GO:0005509", "GO:0005515", "GO:0042803", ...
written 12.8 years ago by Paquet, Agnes500
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Answer: A: OntoCompare Error
... Hi Johannes, OntoCompare will only work with the following probe types: Gene Ontology ids, Affymetrix oligo Ids and Operon human and Mouse oligo ids. Other types will not be recognized and you will get an error. Best, Agnes ________________________________ From: bioconductor-bounces@stat.math.e ...
written 12.8 years ago by Paquet, Agnes500
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question about the value retured by function ontoCompare()
... Hi Ren, GoTools provides 3 ways to count the number of children for each endnode. I will use the Affymetrix data example affylist provided in the package to illustrate the methods. This data object contains 3 sets of ids from Affymetrix hgu133a. "None": for each ennode, return the number of ch ...
go hgu133a probe process gotools oligo written 12.8 years ago by Paquet, Agnes500
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Answer: A: Using ontoCompare with local GO database
... Hi Alessandro, goTools is using accessors build in the GO package from Bioconductor to navigate in the GO DAG, so the GO package is required to run goTools (and ontoCompare). Is there any specific reason for you to use a local install of GO rather than the Bioconductor package? Best, Agnes ______ ...
written 12.9 years ago by Paquet, Agnes500

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