User: Heike Pospisil

gravatar for Heike Pospisil
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Posts by Heike Pospisil

<prev • 31 results • page 1 of 4 • next >
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topGO: add title to the DAG
... Hello Bioconductors, does anybody know how one can add a title to the graphical output of topGO ('showSigOfNodes')? Thanks in advance, Heike -- Pflichtangaben gem?? Gesetz ?ber elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universit?tsklinikum ...
written 10.8 years ago by Heike Pospisil • 310 • updated 4.5 years ago by christian.peikert • 0
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Comment: C: Overlapping genes in subsets of lists
... Hi Thomas, I guess, the latter approach will work. I am going to test this. Thanks to you (and Sean who suggested a similar approach), Heike On Wednesday 08 October 2008 15:23, Thomas Hampton wrote: > I would use the table function in R, which will tell you how many > times gene X appears. ...
written 10.8 years ago by Heike Pospisil • 310
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Overlapping genes in subsets of lists
... Hello there, I have 100 lists of differentially expressed genes, and I am trying to find genes overrepresented in these 100 lists (I call them a 'cluster of genes'). What's worse, I expect not only one cluster of genes, but three or four or five of them. That is why, a simple intersection() will no ...
written 10.8 years ago by Heike Pospisil • 310 • updated 10.8 years ago by Martin Morgan ♦♦ 23k
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Comment: C: topGO question
... Hi Adrian, thanks for your reply. I passed the annFUN.gene2GO and got no errors. allGo contains no NA and no NULL. go_list is a list of character vectors: > str(go_list2) List of 9 $ TM00000001: chr [1:2] "GO:0009058" "GO:0016757" $ TM00000002: chr [1:38] "GO:0003700" "GO:0007275" "GO:00 ...
written 10.9 years ago by Heike Pospisil • 310
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topGO question
... Hello list, I am trying to use topGO for GO enrichment analysis. I have data from an array which is still not supported by BioC (maize array). I have a mapping of genes to GO terms named go_list: $TM00000001 [1] "GO:0009058" "GO:0016757" $TM00000002 [1] "GO:0003700" "GO:0007275" "GO:0005634" "G ...
annotation go topgo written 10.9 years ago by Heike Pospisil • 310 • updated 10.9 years ago by Adrian Alexa • 400
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Problems loading SparseM
... Hello, I am trying to load topGO. SparseM is required by this package. I have successfully installed SparseM (version 0.78), but I did not succeed in loading the SparseM package into R 2.7. Does anybody know a trick for loading SparseM? Thanks in advance, Heike > library(SparseM,lib.loc=my.li ...
topgo written 10.9 years ago by Heike Pospisil • 310 • updated 10.9 years ago by Sean Davis ♦ 21k
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GO over representation analysis
... Hello Bioconductors, I am looking for a method to perfom over representation analysis (Gene Ontology) within R. I have data from the Maize Oligonucleotide Array (two channel) with the GO categories for all probes on this array. I have clustered the genes using Maanova and I am interested in GO over ...
annotation go maanova written 10.9 years ago by Heike Pospisil • 310 • updated 10.9 years ago by Marc Carlson • 7.2k
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Answer: A: How to extract log ratios from two color arrays
... Hello again, I have found the answer. The log ratios can be extracted using con.kmean<-consensus(cluster.kmean,thres,draw=FALSE) con.kmean$data.draw Best, Heike On Friday 22 August 2008 18:29, Heike Pospisil wrote: > Hello BioC list, > > I am analysing 38 two color arrays for a t ...
written 10.9 years ago by Heike Pospisil • 310
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How to extract log ratios from two color arrays
... Hallo BioC list, I am analysing 38 two color arrays for a time course experiment with dye swap (5 time points). I have used maanova for normalisation and macluster() for clustering (see code below). Now, I am wondering how to extract the log ratios (R/G) for each gene for each time point. The cons ...
go hgu133a maanova written 10.9 years ago by Heike Pospisil • 310
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GO.db
... Dear Bioconductors, I am going to use GO annotation libraries. Unfortunately, I did not succed in loading the package GO.db. I have got the following error message: Error in checkDBSCHEMA(dbconn, "GO_DB") : invalid DB schema version (found 0.9, expected 1.0) Error : .onLoad failed in 'loadNamesp ...
annotation go written 11.1 years ago by Heike Pospisil • 310 • updated 11.1 years ago by Sean Davis ♦ 21k

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