User: Mike Schaffer

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Posts by Mike Schaffer

<prev • 9 results • page 1 of 1 • next >
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Limma analysis of focused arrays vs. whole genome arrays
... Hi, The lab I work with has used "whole genome" human arrays (~18,000 genes) for a couple years and I have helped with the analysis using Limma. Now, due to costs, they are now considering switching from whole genome arrays to focused arrays with ~400 genes of interest (selected from the whole-gen ...
normalization limma written 14.4 years ago by Mike Schaffer90 • updated 14.4 years ago by Gordon Smyth38k
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limma, subsets of design matrix and p-values
... I've run limma for a few months and had a question about the p-values being calculated from a large set of data vs. just a subset. All of my 2-color array data is relative to an untreated sample and each is replicated three times. For example: Treatment1 vs untreated x 3, Treatment ...
limma written 14.6 years ago by Mike Schaffer90 • updated 14.6 years ago by Naomi Altman6.0k
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p-value/B-statistic interpretation
... I know this is probably beaten to death, but I can't seem to find a satisfactory answer. How can the p-values/B-statistics from limma be properly interpreted? With assumptions satisfied, an FDR corrected p-value cutoff should produce a list of induced/repressed genes that includes a given percenta ...
limma written 15.0 years ago by Mike Schaffer90
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limma Dye Swap question
... I had a question about how limma handles dye swap experiments. The way we typically run these experiments is to label an aliquot of a test set of (amplified) aRNA with Cy3 and another aliquot of the same aRNA with Cy5. We do the same with the control aRNA and hyb opposite dyes on two slides (i.e. ...
limma written 15.1 years ago by Mike Schaffer90 • updated 15.1 years ago by Ramon Diaz1.1k
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More than one weight with marrayRaw class
... Using marrayRaw, Is there a way to combine two columns of data from a GenePix file into the Weight for a spot? For instance I would like to read in the "Flag" and "F Pixels" columns from the GenePix file to filter out all flagged spots and spots below a threshold size. It doesn't appear this is po ...
marray written 15.9 years ago by Mike Schaffer90 • updated 15.9 years ago by Gordon Smyth38k
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Time series data
... Is there a package capable of visualizing time series data a la Gene Spring? How about for normalizing replicate time series data points? -- Mike ...
written 16.0 years ago by Mike Schaffer90 • updated 16.0 years ago by Vincent J. Carey, Jr.6.3k
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Replicate data and p-values
... I'm fairly new to Bioconductor and had a basic question about *recommended* steps to analyze replicate data. I apologize if this has been covered, but I've scoured the message archives and couldn't find any examples to guide me. I'd like to look at 3 biological replicates of treated vs. untreated ...
multtest oligo written 16.1 years ago by Mike Schaffer90
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Export M vs A Plot Data
... Hi, I've used the Biologists Guide to Using Bioconductor and needed help exporting the data from the M vs. A plots. Can anyone suggest an easy way to get a format such as this in a tab-delimited format: gene [tab] M (unnormalized) [tab] M (normalized) [tab] A (geometric mean of intensity) Also, ...
written 16.1 years ago by Mike Schaffer90 • updated 16.1 years ago by michael watson IAH-C3.4k
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Diagnostic plots error
... Took a few days, but I'm up to speed with R and Bioconductor. I have the individual plots working via X11, but the diagnostic plots are causing me trouble. I'm having a problem that I saw (in the mailing list archives) was related to the layout subroutine. When I run the diagnostic plots, I get t ...
written 16.1 years ago by Mike Schaffer90 • updated 16.1 years ago by michael watson IAH-C3.4k

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