User: Heike Pospisil
Heike Pospisil • 310
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Posts by Heike Pospisil
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... 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 11.1 years ago by
Heike Pospisil • 310
• updated
4.8 years ago by
christian.peikert • 0
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... 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 11.2 years ago by
Heike Pospisil • 310
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... 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 11.2 years ago by
Heike Pospisil • 310
• updated
11.2 years ago by
Martin Morgan ♦♦ 24k
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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 11.2 years ago by
Heike Pospisil • 310
0
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... 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"
$TM00000002
[1] "GO:0003700" "GO:0007275" "GO:0005634" "G ...
written 11.3 years ago by
Heike Pospisil • 310
• updated
11.3 years ago by
Adrian Alexa • 400
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... Hello,
I am trying to load topGO. SparseM is required by this package. I have
successfully installed SparseM (version 0.78), but I did not succeed
in
loading the SparseM package into R 2.7. Does anybody know a trick for
loading
SparseM?
Thanks in advance,
Heike
> library(SparseM,lib.loc=my.li ...
written 11.3 years ago by
Heike Pospisil • 310
• updated
11.3 years ago by
Sean Davis ♦ 21k
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... Hello Bioconductors,
I am looking for a method to perfom over representation analysis (Gene
Ontology) within R. I have data from the Maize Oligonucleotide Array
(two
channel) with the GO categories for all probes on this array. I have
clustered the genes using Maanova and I am interested in GO over ...
written 11.3 years ago by
Heike Pospisil • 310
• updated
11.3 years ago by
Marc Carlson • 7.2k
0
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... Hello again,
I have found the answer. The log ratios can be extracted using
con.kmean<-consensus(cluster.kmean,thres,draw=FALSE)
con.kmean$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 11.3 years ago by
Heike Pospisil • 310
0
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1
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489
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1
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... 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 ...
written 11.3 years ago by
Heike Pospisil • 310
0
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2
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488
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2
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... 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 ...
written 11.5 years ago by
Heike Pospisil • 310
• updated
11.5 years ago by
Sean Davis ♦ 21k
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