Raw data to your experiment is provided in an archive called a DTT.
If you have a large amount of data, your DTT may be broken into several
pieces with extensions like DTT, D02, D03, etc. You must have all of the
files for a single set in order to read any of the data in them. If you do
not
the function Affy (like for the
'old' 3-prime based arrays such as MOE430_2plus).
Thanks again,
Guido
Modified PdInfo2Cdf.R function to create CDF using meta-probesets as unit.
(copy/paste):
PdInfo2Cdf - function( pdpkg, celfile, verbose=TRUE, overwrite=FALSE ) {
This script has been
to execute the
function (for testing purposes):
https://sendit.wur.nl/Download.aspx?id=e0c9eea2-5f72-454c-873d-f1a215f57d1c
Note: link is alive for 5 days, and/or allows max 20 downloads.
Regards,
Guido
library(aroma.affymetrix)
SNIP
pdInfo2Cdf(pd.mogene.1.1.st.v1, MouseBrain_1.CEL);
SNIP
likely is able to do what you want. As Henrik
said, 'oligo' used info directly derived from Affymetrix, and this is
apparently what you want.
HTH,
Guido
Guido Hooiveld, PhD
Nutrition, Metabolism Genomics Group
Division of Human Nutrition
Hi,
To follow up on Henrik's suggestion: we recently have made
Bioconductor-compatible ('unofficial') CDFs for the STv2.0/2.1 arrays as well,
essentially using the PD.Info packages. Please find them here:
http://nmg-r.bioinformatics.nl/
HTH,
Guido
-Original Message-
From: aroma
needed.
Guido
-Original Message-
From: aroma-affymetrix@googlegroups.com
[mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: Friday, December 07, 2012 17:51
To: aroma-affymetrix@googlegroups.com
Subject: Re: [aroma.affymetrix] Gene 2.0 ST arrays
Hi.
On Fri
/gene_1_1_st_ap_tissue_sample_data.zip).
Idem for Affy-provided sample Gene ST v2.1 arrays.
Remarkably, loading Gene ST v1.0 arrays goes fine... (I haven't tested any
other array types yet).
See below for code output (first STv1.0 (=working); followed by STv1.1
(=failing)).
Regards,
Guido
verbose
this, but
currently no fix is available.
- Please post on the aroma.affymetrix mailing list if you have problems using
these files. [http://www.aroma-project.org/]
- Files have been created in January 2013.
* In case of available CEL files.
Hope these are uselful! :)
Regards,
Guido
Hi,
You can obtain a set of sample HuGene 2.0 arrays directly from Affymetrix:
http://www.affymetrix.com/support/downloads/demo_data/human2_0.zip
Regards,
Guido
From: aroma-affymetrix@googlegroups.com
[mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Neetu Tandon
Sent: Wednesday, February
.
Regards,
Guido
From: aroma-affymetrix@googlegroups.com
[mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Neetu Tandon
Sent: Wednesday, February 20, 2013 11:37
To: aroma-affymetrix@googlegroups.com
Subject: Re: [aroma.affymetrix] Re: Gene 2.0 ST arrays
Thanks Guido. but the site says
/CustomCDF/CDF_download.asp#v17
HTH,
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
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
:\aroma.affy.test\annotationData\chipTypes\RaGene-2_1-st), and then copied the
CDF into that dir.
Next I ran the code below.
Note that I am on a Windows machine. Also note that since I don’t have some
RaGene 2.1 CEL files I could not test whether the subsequent normalization goes
fine.
HTH,
Guido
> se
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