User: Groot, Philip de

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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 5.7 years ago by Groot, Philip de630
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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 5.7 years ago by Groot, Philip de630 • updated 5.7 years ago by cstrato3.8k
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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 6.0 years ago by Groot, Philip de630
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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 6.3 years ago by Groot, Philip de630
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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 6.5 years ago by Groot, Philip de630 • updated 6.5 years ago by Benilton Carvalho4.2k
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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 6.7 years ago by Groot, Philip de630 • updated 6.7 years ago by James W. MacDonald47k
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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 6.7 years ago by Groot, Philip de630
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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 7.4 years ago by Groot, Philip de630
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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 7.8 years ago by Groot, Philip de630
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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 8.2 years ago by Groot, Philip de630

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