User: Kevin R. Coombes

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Posts by Kevin R. Coombes

<prev • 14 results • page 1 of 2 • next >
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Comment: C: ReadAffy widget fails for Annotated DataFrame
... Sigh. Actually, when we last taught the course in Fall 2006, the version of R that students got in September was 2.3, since 2.4 came out in October. Having checked more carefully, the ReadAffy widget for phenoData or AnnotatedDataFrames (whichever was current) did *not* work in 2.4, but for a diffe ...
written 11.9 years ago by Kevin R. Coombes140
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ReadAffy widget fails for Annotated DataFrame
... Hi, Why does ReadAffy fail for the AnnotatedDateFrame part of an AffyBatch object? The session snapshot included below shows an error in using tkWidgets for AnnotatedDataFrames. I just upgraded to R 2.5.1 (so I would have the same version as the students in the microarray class I'm teaching), and ...
microarray dyndoc tkwidgets affy widgettools written 11.9 years ago by Kevin R. Coombes140 • updated 11.9 years ago by Martin Morgan ♦♦ 23k
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Answer: A: about two way anova on time and treatment
... Hi, I usually start this kind of analysis, as you did, with per-gene two- way ANOVAs. I then compute p-values for the significance of the complete ANOVA (in effect comparing the full model with the null model), and use some kind of FDR estimate to set a cutoff on the p-values for statistical signif ...
written 12.2 years ago by Kevin R. Coombes140
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Comment: C: Annotating HGU133plus2 genes with number of coding changes
... Hi, An equivalent method (BUM) was also described by Pounds and Morris in Bioinformatics in early 2003. BUM is implemented in OOMPA, which is available at http://bioinformatics.mdanderson.org/software.html, and if I ever feel like I have time to maintain it through the steady pace of new BioConduc ...
written 12.4 years ago by Kevin R. Coombes140
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Answer: A: Combining arrays arrays from different tissues and different labs.
... Hi, Most normalization methods assume (either explicitly or implicitly) something about the distributions of values within each sample. At the very least, they assume that some properties of these distributions are the same. The case of mouse embryos and adult tissues illustrates one of the place ...
written 12.4 years ago by Kevin R. Coombes140
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Answer: A: gap-statistic implementation
... Hi, Rebecka Jornsten at Rutgers wrote a version, and it should still be posted at http://www.stat.rutgers.edu/~rebecka/RCode/. In order to make sure I understood the code, I rewrote it slightly and adapted it to use S4 classes. I haven't posted it anywhere, since I haven't had time to prepare the ...
written 12.5 years ago by Kevin R. Coombes140
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Answer: A: can I use FDR correction with hyperGTest conditional GO method?
... Hi, Take a look at Gold DL, Coombes KR, Wang J, Mallick B. Enrichment analysis in high-throughput genomics--accounting for dependency in the NULL. Brief Bioinform. 2006 Oct 31; [Epub ahead of print] when it comes out. (An earlier version is available as aw tech repor ...
written 12.5 years ago by Kevin R. Coombes140
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Answer: A: continued dye effects, after normalization
... Hi, What kind of arrays are these? We had a similar problem with Agilent arrays, which contain a few hundred positive controls that are the brightest spots in the green channel but are invisibly dark in the red channel. Any normalization in use today makes it look like there is a strong dye effec ...
written 12.6 years ago by Kevin R. Coombes140
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Answer: A: What is a good method for analyzing differential expression from Illumina BeadSt
... Hi, Simon Lin and Pan Du at Northwestern currently have a package for Illumina arrays called "lumi" in beta-test; I'm one of the testers. I'm sure that Simon would be happy to have another tester if you contact him.... In any event, the existing package offers several normalization options, includ ...
written 12.7 years ago by Kevin R. Coombes140
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Answer: A: what metric is used to evalute the error rate?
... Shouldn't there be error bars (i.e., confidence intervals) around those error estimates, that ought to get smaller when you use more samples? Best, Kevin Weiwei Shi wrote: > Hi, there: > > This is a question a little bit off topic but I believe many people > using bioconductor ...
written 12.7 years ago by Kevin R. Coombes140

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