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Denise Mauldin | 1 Nov 2005 02:33

AnnBuilder problem?


Hey all,

I'm having a problem with Annbuilder:

> tempConfig <- tempfile()
> writeSourceUrlConfig(tempConfig) 
> root = "http://sioux.fhcrc.org/MIRROR"
> urlData = readSourceUrlConfig(tempConfig, root)
> origUrls = getOption("AnnBuilderSourceUrls")
> geoUrl = origUrls[["GEO"]] 
> urlData[["GEO"]] = geoUrl
> options(AnnBuilderSourceUrls=urlData) 
> localMirror <- paste(root, "ftp.arabidopsis.org/home/tair/", sep="/")
>
> ABPkgBuilder(baseName="mpedbadm_genbank.txt",
+ baseMapType="gbNRef",
+ pkgName="MPEDB",
+ organism="Mus musculus",
+ otherSrc=c(UG="mpedbadm_unigene.txt"),
+ pkgPath="./",
+ version="0.1",
+ author=list(authors="Denise Mauldin", maintainer="Denise Mauldin <dmauldin@...>"))

Warning message: 
Built for UCSC is not valid! in: getUCSCBuilt(organism)
Error in parseKEGGGenome() : Faild to obtain KEGG organism code

>sessionInfo()
R version 2.2.0, 2005-10-06, sparc-sun-solaris2.9
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Wuming Gong | 1 Nov 2005 02:36
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How to install biomaRt package on Windows XP

Hi list,

I found in bioconductor release information that biomaRt package is
currently not available for Windows. Could anyone tell me whether
there is a way to have current biomaRt source package installed on
Windows XP, or the windows version of biomaRt will be released soon? I
use R 2.2.0.

Thanks,

Wuming
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Bettina Harr | 1 Nov 2005 12:30
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gcrma

dear list,

I would like to decompose the function 'gcrma' into its individual 
elements using the function 'expresso'. Does anyone know which of the 
individual methods (i.e. background correction, pm correction, 
normalization and summarization) I have to use in expresso to get gcrma 
as a result?

Thanks

Tina

_________________________________________________

Bettina Harr
Research Group Leader
Abteilung fuer Evolutionsgenetik
Institut fuer Genetik
Universitaet Koeln
Zuelpicher Strasse 47
50674 Koeln - Germany
new!!!: Tel: ++49 221 470 2324
Fax: ++49 221 470 5975
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Seth Falcon | 1 Nov 2005 15:52

Re: How to install biomaRt package on Windows XP

Hi Wuming,

On 31 Oct 2005, wuming.gong@... wrote:
> I found in bioconductor release information that biomaRt package is
> currently not available for Windows. Could anyone tell me whether
> there is a way to have current biomaRt source package installed on
> Windows XP, or the windows version of biomaRt will be released soon?
> I use R 2.2.0.

You might try contacting the package maintainer (see the DESCRIPTION
file inside the source package).  He has had success building Windows
binaries of the package by hand.  We have not, yet, had success
building the package as part of our automated build process.

Best,

+ seth
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Jenny Drnevich | 1 Nov 2005 16:01
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Re: gcrma

Here is one solution to do it piece by piece, although not in expresso:

First, modify the gcrma function to just do the background correction. Type:

 > mygcrma <- edit(gcrma)

and change the last line to read:

return(object)

Then call:

 >gc.affybatch <- mygcrma(raw.affybatch)

and you'll get an affybatch object with GC background corrected data.

You can then do quantile normalization on this (or any other affybatch) by 
simply calling:

 > gcnorm.affybatch <- normalize(gc.affybatch)

To just do the summarization on any affybatch, try:

gcnorm.eset <- rma(gcnorm.affybatch, background=F, normalize=F)

You can also turn off background correction and normalization in expresso, 
but the rma routine is faster. I don't think you can turn off summarization 
in expresso - see ?expresso.

Cheers,
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szhan | 1 Nov 2005 20:28
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How to retrieve the genomic positions and /or orders of probes in the probe set

Hello, Experts,
I have obtained single probe-level data from affybatch object (mydata)using the
script:
library(affy)
mydata<-ReadAffy()
mypm<-pm(mydata)
mymm<-mm(mydata)
myaffyids<-probeNames(mydata)
probedata<-data.frame(myaffyids, mypm, mymm)
Now I want to retrieve the genomic positions and/or orders of probes in each
probe set listed by myaffyids and add them to data frame( probedata).
Could you please help me out?
Thank you in advance!
Joshua
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Jenny Drnevich | 1 Nov 2005 20:31
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E. coli problems: bimodality and gcrma

Hello everyone,

I am starting to analyze a dataset from Affymetrix's E.coli genome 2.0 
arrays, and I'm running into several weird things. This is the first time 
I've handled prokaryotic data, so I don't know if that's the reason it 
looks so different from most eukaryotic data I've seen. I would really 
appreciate it if anyone with E. coli experience would be willing to have an 
extended discussion off-line. Additionally, here are two issues on which 
I'd love some comments:

1. The histograms of the raw pm & mm values are bimodal (see 
ftp://keck1.biotec.uiuc.edu/pub/Drnevich/Ecoli/ for output from 
signalDist). The most extreme array (# 9) had some problems with the 
labeling and hybridization, but it does appear to be at the end of a 
continuum. Looking through the Bioconductor archives, others have commented 
that bimodality may not be a problem in itself, but I wonder if anyone else 
has seen data this extreme or would be suspicious? The five arrays that 
different than the rest are from an different experimental treatment, which 
leads me to believe that this might be real data...

2. Applying bg.adjust.gcrma to the data results in almost zero expression 
for all pm probes! (see link above). I doubt that all the expression is due 
to non-specific binding and/or probe affinity. Is it likely that the 
different labeling of prokaryotic samples (N-terminus) would
render gcrma background correction unusable?

Thanks so much for any comments!
Jenny

Jenny Drnevich, Ph.D.
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Robert Gentleman | 1 Nov 2005 20:41

Re: How to retrieve the genomic positions and /or orders of probes in the probe set

Have you looked at the useProbeInfo vignette in the annotate package?

szhan@... wrote:
> Hello, Experts,
> I have obtained single probe-level data from affybatch object (mydata)using the
> script:
> library(affy)
> mydata<-ReadAffy()
> mypm<-pm(mydata)
> mymm<-mm(mydata)
> myaffyids<-probeNames(mydata)
> probedata<-data.frame(myaffyids, mypm, mymm)
> Now I want to retrieve the genomic positions and/or orders of probes in each
> probe set listed by myaffyids and add them to data frame( probedata).
> Could you please help me out?
> Thank you in advance!
> Joshua
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@...
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> 

--

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
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Denise Mauldin | 1 Nov 2005 21:32

Re: AnnBuilder problem?


The end of my previous message had an error.  The urlData[["GO"]] is 
actually as follows and still gives the list error.

> urlData[["GO"]]
[1] "http://sioux.fhcrc.org/MIRROR/archive.godatabase.org/latest"
> class(urlData[["GO"]])
[1] "character"
> mode(urlData[["GO"]])
[1] "character" 

Thanks,
Denise
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Assa Yeroslaviz | 2 Nov 2005 13:47
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attributes of SAM files

Hi,

Is there a way of extracting ONLY a list of the attributes of an output file
from the siggenes package?

After doing a sam calculation:
>A.out <- sam(AE0627999.data, AE0627999.cl,
B=200,rand=123,gene.names=matrix_all_names[,2])

I wanted than to look at the attributes of the file:
>attributes(A.out)

The List I've got is to long to be observed in my GUI window, so I would like to
know, if there is a possibility to only see the titles of the attributes and not
the whole list.

THX,

Assa

--
Assa Yeroslaviz
Lötzenerstr. 15
51373 Leverkusen
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