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User: Groot, Philip de
Groot, Philip de • 630
- Reputation:
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- Last seen:
- 6 years, 1 month ago
- Joined:
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Posts by Groot, Philip de
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Comment:
C: xps: hugene11 chip gives problems
... Dear Christian,
Thank you very much! I was thinking that it must have been something
in the CEL-file itself, but it turns out to be the filename! I'll
adapt the script on our production server to fix the issue. I have to
mention that we use xps for quite some years now. We never encountered
this is ...
written 6.1 years ago by
Groot, Philip de • 630
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... Hi Christian,
I am trying to do an analysis using xps and the hugene11 chip.
However, I run into problems for which I need your help.
I created a small test-script to demonstrate the problem:
library(xps)
scheme <-
root.scheme("/local2/R-2.15.2/library/xps/schemes/hugene11stv1.root")
x.xps < ...
written 6.1 years ago by
Groot, Philip de • 630
• updated
6.1 years ago by
cstrato • 3.9k
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... Hi junhui,chen,
I make the CDFs available on:
http://nmg-r.bioinformatics.nl/NuGO_R.html
Direct link:
Linux: http://nmg-r.bioinformatics.nl/Custom_CDF_DB_V15.1.0/src/contri
b/hugene11stv1cdf_2.5.0.tar.gz
Windows: http://nmg-r.bioinformatics.nl/Custom_CDF_DB_V15.1.0/bin/wind
ows/contrib/2.15/hugen ...
written 6.4 years ago by
Groot, Philip de • 630
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... I created some CDF-files for these chips that you can also use (not
sure on the r4 though):
http://nmg-r.bioinformatics.nl/NuGO_R.html
Regards,
Dr. Philip de Groot
Bioinformatician / Microarray analysis expert
Wageningen University / TIFN
Netherlands Nutrigenomics Center (NNC)
Nutrition, Metabol ...
written 6.7 years ago by
Groot, Philip de • 630
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... Dear Benilton,
I tried to create the pdInfoBuilder packages for the Affymetrix
Arabidopsis ST 1.0 arrays and did run into a problem that I cannot
solve myself. I guess that it also affects the Arabidopsis ST 1.1
cartridges, so you might want to take a look. I pasted the appropriate
information be ...
written 6.9 years ago by
Groot, Philip de • 630
• updated
6.9 years ago by
Benilton Carvalho • 4.3k
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... Dear James,
I apologize for the email from yesterday. I totally agree with your
points. In addition, I really appreciate the effort that is undertaken
in establishing the oligo package. I am using the library myself
regularly!
However, there is a reason why I reacted this way. The affy problem
has ...
written 7.1 years ago by
Groot, Philip de • 630
• updated
7.1 years ago by
James W. MacDonald ♦ 49k
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... Hello all,
Just to be sure:
>If you follow the discussion that Mike linked to, this has been
corrected in the devel version of the affy package. I made this change
because >it didn't have an adverse effect on the intended target of
the affy package, which is the 3' biased arrays. I have not ...
written 7.1 years ago by
Groot, Philip de • 630
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... Hello all,
I run into the following problem. Regularly, I need to create affyPLM
QC images as created by the affyPLM library and image(). I found out
that in R-2.13.0 the creation of these images are very slow when I
write them to bitmap(). Actually, I do use the function screenpng as
provided by s ...
written 7.8 years ago by
Groot, Philip de • 630
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... Hello all,
I also reacted yesterday. Apparently, it came not through. I created a
CDF-environment for Mouse Gene ST v 1.1 that properly takes the
dimensions into account. I attached the source file to this email.
People whom need a windows library should contact me :-).
Anyway: to utilize the cdf- ...
written 8.2 years ago by
Groot, Philip de • 630
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Comment:
C: Illumina chip probe sequences
... Hello all,
No, probe libraries for Illumina are not available. They should not be
because you can export the probe sequences in beadstudio. Exporting
those is really helpful in properly analysing illumina arrays in the
lumi package!
Probe sequences can be found on the Illumina annotation files on ...
written 8.6 years ago by
Groot, Philip de • 630
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For tcltk problem under Linux (both 32 and 64 bits)
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