Hi,
I was a little curious to know what these scripts are able to
construct/convert, so I had a quick look at the codes.
@ Elizabeth (or others):
Although I am not planning to use these (yet), there is one thing that
(naively?) did not become immediately clear to me: what is the expected content
of the file annotExonBoundaries that is required for the (1st) function
annotateProbesets.R, (and how would generate such file)?
From the description in the script:
exonBoundariesFile=file name of deliminated file with the exon boundaries that
you want to map the probesets to.
##annotExonBoundaries-file.path(outdir,exonBoundaries_proteinCoding_20080819.txt)
Thanks,
Guido
-
Guido Hooiveld, PhD
Nutrition, Metabolism Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
tel: (+)31 317 485788
fax: (+)31 317 483342
email: guido.hooiv...@wur.nl
internet: http://nutrigene.4t.com
http://scholar.google.com/citations?user=qFHaMnoJ
http://www.researcherid.com/rid/F-4912-2010
-Original Message-
From: aroma-affymetrix@googlegroups.com
[mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: Wednesday, January 22, 2014 21:15
To: aroma-affymetrix@googlegroups.com
Subject: Re: [aroma.affymetrix] Construct cdf file from pgf, clf and gene
mapping file
Alright, so Elizabeth Purdom found the missing files and kindly sent them to
me. I've now uploaded them the http://aroma-project.org server and updated the
links on http://aroma-project.org/node/40 accordingly.
Hope this helps
Henrik
On Tue, Jan 21, 2014 at 3:35 PM, Henrik Bengtsson
henrik.bengts...@aroma-project.org wrote:
Hi,
thanks for reporting on this.
On Mon, Jan 20, 2014 at 2:09 PM, Guilherme Rocha gvro...@gmail.com wrote:
Dear all,
Does anybody know of any good tools for constructing a cdf file from
affy pgf and clf files?
It appears that such tools exist:
http://www.aroma-project.org/node/40
The problem is the following 3 links in above address are broken:
1)http://bcgc.lbl.gov/cdfFiles/flat2Cdf.R
Flat2cdf.R (constructs a cdf file from a flat file)
It turns out that that file is the same as
http://bioinf.wehi.edu.au/folders/mrobinson/exon/flat2Cdf.R
I've update the webpage to link to that instead (for now).
2)http://bcgc.lbl.gov/cdfFiles/combineProbeInfo.pl
combineProbeInfo.pl (combines pgf and clf files into single flat file
with each row containing most of the information needed for each
probe)
Unfortunately, I cannot locate this elsewhere.
3)http://bcgc.lbl.gov/cdfFiles/addGeneId.pl
addGeneId.pl (takes output of previous pl script and merge it with
probeset-gene map to generate flat file needed by flat2cdf)
Unfortunately, same for this one (and the other links on that page).
If you can generate a flat text-files as on illustrated on that
page, you could still create a CDF. However, note that the flat2Cdf()
function is rather specific to gene-exon chip types, so if you're
looking to create other types of CDF files, it won't work (at least
not out of the box).
I've updated http://aroma-project.org/node/40 with the following note:
Note: Several of the links to the external third party R and Perl
scripts are broken, i.e. annotateProbesets.R,
convertProbesetCSV_differentInput.pl, selectProbes.pl
combineProbeInfo.pl, addGeneId.pl. If you have any of these files
sitting around, please consider sending them to use. Thanks /HB
2014-01-20
Thanks,
Henrik
Any help greatly appreciated.
Thanks,
Guilherme Rocha
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