User: Dennis.Burian@faa.gov

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Posts by Dennis.Burian@faa.gov

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Bioconductor Digest, Vol 100, Issue 28
... >Hi Everyone >I use custom designed chicken high-density multiplex one channel microarray (NimbleGen 12x135K). My usual >pipeline includes mostly oligo, arrayQualityMetrics, preprocessCore, genefilter, GeneSelector and limma. So >far I only worked with simple design, 2 conditions; contr ...
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PLPE error
... Hello, I'm using PLPE to compare six samples, two replicates. I'm getting an error that has me stumped. I'm including the sessionInfo output and the two input files I call for the function. Also, if the developers could help me with the data.type argument to use for Affy microarray data. Thanks ...
microarray affy lpe plpe written 10.4 years ago by Dennis.Burian@faa.gov90
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model.matrix question
... For purposes of creating an experimental design in limma, are model.matrix and modelMatrix essentially the same or is one preferred over the other? What is the $qr matrix? Thanks, Dennis Burian, Ph.D. Functional Genomics Group Civil Aerospace Medical Institute, AAM-610 6500 S. MacArthur Blvd. Okl ...
limma written 11.1 years ago by Dennis.Burian@faa.gov90
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rowQ error
... Sorry, my intent was to return it to the list. Needing devel explains why a cutoff of 0.5 only returned 674 probe sets with nsFilter. That had me scratching my head plenty but after the brain fade with rowQ, I wasn't going to ask any questions until I was more sure of my footing with the genefilte ...
cancer genefilter written 11.4 years ago by Dennis.Burian@faa.gov90
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rowQ error
... I am using rowQ to filter on interquartile range on HgU133 plus2 Affy chips. The following is my setup and a description of the ExpressionSet, and at the end, the error I'm getting "which is larger than the number of rows" which is, of course, not true since both 13669 and 41006 are less than 546 ...
written 11.4 years ago by Dennis.Burian@faa.gov90 • updated 11.4 years ago by rgentleman5.5k
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Comment: C: boxplots on summarized data
... That's it, thanks for the quick reply. Dennis Burian, Ph.D. Functional Genomics Group Civil Aerospace Medical Institute, AAM-610 6500 S. MacArthur Blvd. Oklahoma City OK 73169 405-954-6087 dennis.burian at faa.gov Jenny Drnevich To ...
written 11.4 years ago by Dennis.Burian@faa.gov90
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boxplots on summarized data
... I'm having a time generating boxplots across chips on summarized data for more than one gene at a time. I want a set of boxplots for a subset of the genes, say the 10th to the 20th genes in the ExpressionSet. I expect this is an R list question but since the data is an expression set decided to p ...
written 11.4 years ago by Dennis.Burian@faa.gov90 • updated 11.4 years ago by Joern Toedling720
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filtering on variance
... I was planning to filter on summarized/normalized Affy expression data and keep the genes in the high 50% of variance, but saw the recent paper on an algorithm called FLUSH in NAR that filters on probe level data. What is the recommendation of the collective BioC consciousness about the stage in d ...
probe affy written 11.5 years ago by Dennis.Burian@faa.gov90
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Title for a matplot
... Dear all, I ran the following command to add a title to a matplot the logic being that the help for matplot refers the reader to the help for plot. As you can see, matplot doesn't recognize the title argument. Any other ideas for a way to get a title added to the matplot? > matplot(pm(Buc ...
written 12.2 years ago by Dennis.Burian@faa.gov90 • updated 12.2 years ago by James W. MacDonald50k

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For boxplots on summarized data

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