User: Kevin R. Coombes

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Posts by Kevin R. Coombes

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Comment: C: Some Genefilter questions
... Hi, It may be worth pointing out that a related question can have a huge impact on normalization of certain glass arrays. One of the standard protocols on the Agilent 44K human arrays causes several hundred control spots to light up extremely brightly in the green channel, but remain completely off ...
written 12.8 years ago by Kevin R. Coombes140
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Comment: C: getGEO
... Slow means REALLY SLOW. I recently downloaded both a SOFT file and a MINiML file for the same data set (27 two-color glass arrays with 23,184 spots per array) from GEO. Reading the SOFT format with GEOquery took more than an hour-and-a-half. Unzipping and reading the TSV files in the MINiML format ...
written 12.9 years ago by Kevin R. Coombes140
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Comment: C: nested design in limma?
... It depends on the overall goal. If you are only comparing two groups of samples (A and B) and never want to compare any of the data with anything else, then it is more efficient to use a design that runs A against B on the same slide. In that case, I believe some A samples should be run in the Cy3 ...
written 13.6 years ago by Kevin R. Coombes140
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Answer: A: Hier.Clustering: group size effect
... If you already know the groups, then what's the point of doing clustering? More precisely, what biological question do you think you are answering with this method? Kevin Heike Pospisil wrote: > Hello, > > I have a question concerning hierarchical clustering and the effect of grou ...
written 13.6 years ago by Kevin R. Coombes140

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