User: Francois Collin

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Posts by Francois Collin

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Answer: A: 2 Courses Near You - (1) Introduction to R/S+ programming: Microarrays Analysis
... who is xlsolutions-corp??? --- Sue Turner wrote: > XLSolutions Corporation (www.xlsolutions-corp.com) > is proud to announce: > > (1) Introduction to R/S+ programming: Microarrays > Analysis and Bioconductor > > *** San Francisco / July 17-18, > 2006 ** ...
written 13.5 years ago by Francois Collin130
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Answer: A: affy chips' quality control question
... Hello Ren, Being puzzled in this case is a good thing as there are no hard and fast rules as to which outlier chips should be excluded from an analysis. In a sense, the answer really depends on the analysis in question. One way to answer the question of which chips should be excluded, or treated di ...
written 13.8 years ago by Francois Collin130
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Answer: A: programming problem: running many ANOVAs
... Yes, there is a way to avoid all of the overhead in lm(). As you are fitting the same model to the data for all genes, you should only have to get the qr decomposition of your design matrix once. Here are some ideas for code - with someting like this you should get the same results that you would ...
written 15.6 years ago by Francois Collin130
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Comment: C: unbalanced factorial design
... Running lme on a single probe set takes about 20 minutes computing time on my PC. I'm running R on windows, which I know can run into memory management problems, but this problem appears to be completely cpu bound. The model that I'm fitting has repeated measures, 6 Visits per Subject, for 20 Subj ...
written 15.8 years ago by Francois Collin130
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Comment: C: Statistical comparison of low replicate affy data
... Paul, The weights are derived from the model fit residuals - they are transformations of the residuals standardized by the model fit residual variance (fit here being probe set specific). Weights will be 1.0 if the residuals are small compared to the residual variance, and then decrease toward zero ...
written 15.8 years ago by Francois Collin130
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Answer: A: iterative gcrma on 92 slides?
... Having to analyze large sets of chips on a PC equipped with little memory, I had to deal with this issue all the time. Getting rma or gcrma expression summaries is typcally viewed as a three step process: background correction, normalization and model fitting. The latter step, can be further divi ...
written 15.9 years ago by Francois Collin130
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Re: Affy cel file processing - system requirements
... Dear list: I know this has been discussed before, but I can't open the link to the Bioconductor Archives. My question is regarding the key system requirements to be able to "comfortably" analyze Affy cel files. The bottleneck on my machine (more like a dead end) is trying to run bg.adjust.gcrma(). ...
affy written 15.9 years ago by Francois Collin130 • updated 15.9 years ago by James W. MacDonald52k
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Affy cel file processing - system requirements
... Dear list: I know this has been discussed before, but I can't open the link to the Bioconductor Archives. My question is regarding the key system requirements to be able to "comfortably" analyze Affy cel files. The bottleneck on my machine (more like a dead end) is trying to run bg.adjust.gcrma(). ...
affy written 15.9 years ago by Francois Collin130
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Comment: C: RNA digestion plots
... We should keep in mind that systematic differences detected among probe intensities within a probe sets are tiny in comparison to the typical variation in intensity observed among probes within a probe set. Systematic differences are detectable because we are summarizing probe intensities by locati ...
written 16.1 years ago by Francois Collin130
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Comment: C: Affy: gene filtering before or after normalization??
... Thanks for the referecne to our work, Wolfgang. Hope it isn't considered spamming if I put a link to a poster presentation: http://www.affymetrix.com/corporate/events/seminar/microarray_workshop .affx I concur with Wolfgang that residuals from fits provide great quality assessment opportunities. ...
written 16.2 years ago by Francois Collin130

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