User: Groot, Philip de

gravatar for Groot, Philip de
Reputation:
630
Status:
Trusted
Location:
Last seen:
5 years, 10 months ago
Joined:
13 years, 5 months ago
Email:
p*************@wur.nl

Posts by Groot, Philip de

<prev • 63 results • page 1 of 7 • next >
0
votes
1
answers
551
views
1
answers
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 5.8 years ago by Groot, Philip de • 630
0
votes
1
answer
551
views
1
answer
xps: hugene11 chip gives problems
... 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 < ...
microarray annotation xps written 5.9 years ago by Groot, Philip de • 630 • updated 5.9 years ago by cstrato • 3.9k
0
votes
2
answers
625
views
2
answers
Answer: A: CDF file for Mouse Gene 1.1 ST Array
... 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 6.2 years ago by Groot, Philip de • 630
0
votes
2
answers
438
views
2
answers
Comment: C: XPS package working with Affymetrix GeneChip 1.0 ST at gene level
... 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 6.5 years ago by Groot, Philip de • 630
0
votes
1
answer
732
views
1
answer
pdInfoBuilder fails on the new Arabidopsis Gene ST 1.0 & 1.1 arrays
... 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 ...
annotation oligo pdinfobuilder oligoclasses written 6.7 years ago by Groot, Philip de • 630 • updated 6.7 years ago by Benilton Carvalho • 4.3k
0
votes
1
answer
533
views
1
answer
affy : ReadAffy() fails on HuGene-1_1-st-v1 chips
... 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 ...
microarray cdf affy makecdfenv process oligo cycle written 6.8 years ago by Groot, Philip de • 630 • updated 6.8 years ago by James W. MacDonald ♦ 48k
0
votes
2
answers
830
views
2
answers
Comment: C: affy : ReadAffy() fails on HuGene-1_1-st-v1 chips
... 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 6.8 years ago by Groot, Philip de • 630
0
votes
0
answers
373
views
0
answers
bitmap() extremely slow!
... 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 ...
microarray affyplm written 7.5 years ago by Groot, Philip de • 630
0
votes
2
answers
1.1k
views
2
answers
Comment: C: CDF file for Mouse Gene 1.1 ST Array
... 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 8.0 years ago by Groot, Philip de • 630
0
votes
2
answers
642
views
2
answers
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 8.3 years ago by Groot, Philip de • 630

Latest awards to Groot, Philip de

No awards yet. Soon to come :-)
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 160 users visited in the last hour