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Prof. Roland Wagner | 17 May 14:48
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BIRD 08: Call for participants

Call for participants

BIRD'08
2nd International Conference
on
Bioinformatics Research and Development
www.birdconf.org <http://www.birdconf.org>

Technical University of Vienna, Austria
July 7-9, 2008

Best regards
Roland Wagner

--

-- 
Univ. Prof. Dr. Roland Wagner
Johannes Kepler Universität Linz
A-4040 Linz
Austria
Europe

Tel.: +43 676 84673210
Fax: +43 732 24689308
rrwagner@...

Director of the Institute of Applied Knowledgeprocessing  (FAW)
sec1: Monika Neubauer
Tel.: +43 676 84673212
Fax.:+43 732 2468 9308
mneubauer@...
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Balko, Justin M | 16 May 22:56
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GEOquery package

Hello,
Im running R 2.5.0
When I load the R package GEOquery, I am getting the following error:

the part of the args list of 'list' being evaluated was:
   (header = list(), )
Error in makeClassRepresentation(Class, properties, superClasses, prototype,  :
        element 2 is empty
Error : unable to load R code in package 'GEOquery'
Error: package/namespace load failed for 'GEOquery'

Seems to have installed fine, or maybe not.

package 'GEOquery' successfully unpacked and MD5 sums checked
updating HTML package descriptions

Any insight?
Thanks!

al({pkg <- select.list(sort(.packages(all.available = TRUE)))
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
the part of the args list of 'list' being evaluated was:
   (header = list(), )
Error in makeClassRepresentation(Class, properties, superClasses, prototype,  :
        element 2 is empty
Error : unable to load R code in package 'GEOquery'
Error: package/namespace load failed for 'GEOquery'

Justin Balko, PharmD
Graduate Student
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Heidi Dvinge | 16 May 19:44
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Bug in base.profiles.nc (gcrma)?

Hi,

I'm trying to use gcrma with affinity.source= "local", and a predefined
set of NCprobes with gcrma v. 2.12.0. However, I'm running into problems
with the sub-function base.profiles.nc. I think that where it says:

    if (length(seqs) < length(NCprobe)) {
        cat("\nNote: some of your negative control probes do not have
sequence information\n")
        subIndex2 <- match(c(xy2indices(p$x, p$y, cdf = cdfpackagename),
            xy2indices(p$x, p$y + 1), cdf = cdfpackagename),
            NCprobe)
        subIndex2 <- subIndex2[!is.na(subIndex2)]
        bgy <- bgy[!is.na(subIndex1), ]
    }

isn't is supposed to be:

    if (length(seqs) < length(NCprobe)) {
        cat("\nNote: some of your negative control probes do not have
sequence information\n")
        subIndex2 <- match(c(xy2indices(p$x, p$y, cdf = cdfpackagename),
            xy2indices(p$x, p$y + 1, cdf = cdfpackagename)),       #
moving the ")" here
            NCprobe)
        subIndex2 <- subIndex2[!is.na(subIndex2)]
        bgy <- bgy[!is.na(subIndex1), ]
    }

Thanks
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Hartmut Scheel | 16 May 17:49
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heatmap.2 - centering the color ramp


Hello,
a short question. How would one manage to have the color range centred
around 0 instead of assigning the extreme colors (say red and green) to
the lowest and largest value? Black should be at "0" and not at the mean
value between the largest and the smallest value. I need to compare
different heatmaps.

Thanks for any suggestion
Hartmut

Here some simple Data:
mdat <-
matrix(c(1.09761079662642,0.552868871011303,0.236339539168374,-0.1568201
09742826,0.0908534304511135,-0.500217879852688,-0.182786075741673,-0.248
107861595691,-0.362157939675895),ncol=3,nrow=3,dimnames=list(c("C1","C2"
,"C3"),c("T1","T2","T3")))

 heatmap.2(mdat,Rowv=NULL,Colv="Rowv",
scale="none",col=greenred(75),key=TRUE, symkey=FALSE,
density.info="none", trace="none",dendrogram="none")

	[[alternative HTML version deleted]]

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Davis, Wade | 16 May 16:49
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lumiMouseV1 trouble

Hello BioC community:

I am having trouble with lumiMouseV1. I am able to go from ID ->
ENTREZID via lumiMouseV1ENTREZID:

> entrezIds <- mget(featureNames(lumi.N), envir =
lumiMouseV1ENTREZID,ifnotfound=NA)
> head(entrezIds)
$iSh39ilew_g4tR.A18
[1] 78928

$`GI_10304988-S`
[1] NA

$oS6QgIgopJKKQ4S9Ko
[1] 16728

$`GI_12963686-S`
[1] NA

$`GI_12963764-I`
[1] NA

$`GI_13385605-S`
[1] NA

However, when I do the same for ID -> GO, every entry is NA.

> haveGO <-mget(featureNames(lumi.N), lumiMouseV1GO,ifnotfound=NA)
> head(haveGO)
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Mark Kimpel | 16 May 02:32
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question on affyQCReport vignette

I am a satistified user of affyQCReport and want to make sure that I include
the appropriate citations in a paper I am submitting. As this package is
sort of a wrapper for some other packages and the vignette does not include
any references beyond that of Gautier, et al, which describes the affy
package, could someone be kind enough to supply me with the appropriate
citations?

In general, it is sort of a pet peeve of mine that developers rightly want
their work cited, but too often I feel that the citation information on the
help(package == "foo") page is imcomplete. Would it be presumtuous to ask
for developers to include a handy list of citations for their packages,
package dependencies, etc. as part of the general help page for their
package? I don't know what the official R/BioC policy is on this, but it
would be extremely helpful both to users and those whose original ideas are
incorporated into R/BioC.

And, if I"ve missed something obvious, point me in the right direction,
spank me with a wet noodle and accept my apologies.

Thanks,
Mark

--

-- 
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN 46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)
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martin sikora | 15 May 17:55
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RCurl compilation error - fedora 7

dear list members,

i'm having a problem installing the biomaRt package on my linux machine, 
due to the fact of a compilation error with RCurl. i am using R 2.6.2 on 
fedora 7, and this is the output i get:

gcc -m32 -std=gnu99 -I/usr/include/R -I/usr/include/R  
-DHAVE_LIBIDN_FIELD=1 -I/usr/local/include    -fpic  -O2 -g -pipe -Wall 
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic 
-fasynchronous-unwind-tables -c base64.c -o base64.o
In file included from base64.c:1:
Rcurl.h:52: error: expected specifier-qualifier-list before ?cetype_t?
base64.c: In function ?R_base64_decode?:
base64.c:25: warning: pointer targets in assignment differ in signedness
base64.c:39: warning: pointer targets in passing argument 1 of 
?Rf_mkString? differ in signedness
base64.c: In function ?R_base64_encode?:
base64.c:60: warning: pointer targets in assignment differ in signedness
make: *** [base64.o] Error 1

as far as i know i have all the necessary libraries installed:

$ yum list installed | grep libxml
libxml2.i386                             2.6.31-1.fc7           
installed      
libxml2-devel.i386                       2.6.31-1.fc7           
installed      
libxml2-python.i386                      2.6.31-1.fc7           
installed
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Vladimir Morozov | 15 May 17:47
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GSEABase how to map gene symbols to mouse EntrezId or Affy

Hi

Any suggestions how to map  gene symbols to mouse EntrezId(preffered) or
Affy. 
mapping to Entez apparently is not supported by GSEABase
> mapIdentifiers(gss,EntrezIdentifier())
Error in .mapIdentifiers_isMappable(from, to) : 
  unable to map from 'Symbol' to 'EntrezId'
    neither GeneIdentifierType has annotation
Error in GeneSetCollection(lapply(what, mapIdentifiers, to, ..., verbose
= verbose)) : 
  error in evaluating the argument 'object' in selecting a method for
function 'GeneSetCollection'

 
Mapping to Affys works for human, but not for mouse
> mapIdentifiers(gss, AnnotationIdentifier("hgu95av2.db"))
GeneSetCollection
  names: chr5q23, chr16q24 (2 total)
  unique identifiers: 35089_at, 35090_g_at, ..., 35807_at (79 total)
  types in collection:
    geneIdType: AnnotationIdentifier (1 total)
    collectionType: BroadCollection (1 total)
> mapIdentifiers(gss, AnnotationIdentifier("mouse4302.db"))
GeneSetCollection
  names: chr5q23, chr16q24 (2 total)
  unique identifiers:  (0 total)
  types in collection:
    geneIdType: AnnotationIdentifier (1 total)
    collectionType: BroadCollection (1 total)
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Vladimir Morozov | 15 May 16:51
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GSEABase error in parsing msigdb_v2.5.xml

Hi,

I get error reading the last vesrsion of Broad msigdb . Is it supposed
to work?

> gss <- getBroadSets('/data/PathDB/msigdb_v2.5.xml')
Error: 'getBroadSets' failed to create gene sets:
  invalid BroadCollection category: 'c5'
> traceback()
6: stop("'getBroadSets' failed to create gene sets:\n  ",
conditionMessage(err), 
       call. = FALSE)
5: value[[3]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       geneSets <- unlist(mapply(.fromXML, uri, "//GENESET", factories, 
           SIMPLIFY = FALSE, USE.NAMES = FALSE))
   }, error = function(err) {
       stop("'getBroadSets' failed to create gene sets:\n  ",
conditionMessage(err), 
           call. = FALSE)
   })
1: getBroadSets("/data/PathDB/msigdb_v2.5.xml")
> packageDescription('GSEABase')
Package: GSEABase
Type: Package
Title: Gene set enrichment data structures and methods
Version: 1.2.0
Author: Martin Morgan, Seth Falcon, Robert Gentleman
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Mark Dunning | 15 May 16:38
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Multiple colours in GenomeGraphs?

Hi all,

I have just started using the GenomeGraphs package, which I think is a
really good piece of software :)

I am using the package to plot expression values across a genomic
region. However, it seems to plot all points on the same "track" in the
same colour? I was wondering if it is possible to use different colours
to highlight particular probes I am interesting in, (or use different
plotting characters). I thought something like:

dp=DisplayPars(color=c("red","blue")) might work, but it just produced
one colour. Apologies if there is already the ability to do this, but I
didn't see anything so far.

Many thanks,

Mark

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Ruppert Valentino | 15 May 15:38
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Re: converting gene name to affy probe


Hi Sebastien,

Thanks for the tip :

ls(hgu133aSYMBOL)[mget(ls(hgu133aSYMBOL), hgu133aSYMBOL) %in% gensym]
works fine

I would be grateful if you can tell me how to convert Affy probe to gene name? i.e. the opposite way

I tried using hgu133aGENENAME but that didn't work as its using the description. 

How do I use hgu133aSYMBOL to get gene name from affy probe.

Many thanks

Ruppert

> Date: Tue, 6 May 2008 13:07:22 +1000> From: seb@...> To:
ruppert7@...> Subject: Re: [BioC] converting gene name to
affy probe> > Ruppert Valentino wrote:> > Hello, I am trying to convert a file of gene names to
corresponding affy probe names. I managed to write a script that puts the genes in an array then I use the
feat = getFeature(symbol = gensym, type = "affy_hg_u133a", mart = mart) in biomaRt however I seem to hit a
snag when there is more than probe for a gene name. Does anyone know of an existing script that can do this?
thanks Ruppert> > _________________________________________________________________> > Win
Indiana Jones prizes with Live Search> >> > [[alternative HTML version deleted]]> >> >
_______________________________________________> > Bioconductor mailing
  list> > Bioconductor@...> >
https://stat.ethz.ch/mailman/listinfo/bioconductor> > Search the archives:
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