User: Ben Bolstad

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Ben Bolstad1.1k
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Posts by Ben Bolstad

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Comment: C: R-2.2 and BioConductor 1.7: changes in GC-RMA and fitPLMprocedures
... Philip, The issue I am raising here is that I have seen a few situations where there is a large clear artifact on a chip, reflected in the NUSE and RLE statistics as being of poorer quality, using the standard procedure, but when called with the GCRMA background the artifacts are gone and there is ...
written 14.0 years ago by Ben Bolstad1.1k
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Answer: A: R-2.2 and BioConductor 1.7: changes in GC-RMA and fitPLMprocedures
... Hi, It is good to hear that the results agree. The function bg.correct.gcrma was introduced into the affyPLM package at the time of the previous BioC release (1.6) as an aid to allow you to use the GC-RMA background with the fitPLM, threestep, threestepPLM etc (ie you could supply background.method ...
written 14.0 years ago by Ben Bolstad1.1k
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Answer: A: Replictes quality
... You might want to investigate the affyPLM package for general quality assessment of Affymetrix arrays. The simpleaffy package provides the Affymetrix QC measures (eg present present, etc). Ben On Thu, 22 Sep 2005, Marco Gentilini wrote: > Well, I didn't say I'm using Affymetrix GeneChip > T ...
written 14.1 years ago by Ben Bolstad1.1k
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Answer: A: CEL file conversion for custom CDF arrays gives segmentation fault when run
... Could you please give the output of sessionInfo()? It looks to me that perhaps your R version (and thus probably your versions of the BioC packages) is older (basing this off the path name in your output below). It would also be helpful if you could describe a little bit better what you mean by cus ...
written 14.1 years ago by Ben Bolstad1.1k
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Answer: A: ArrayAssist vs. Bioconductor
... Hi Bruz, I can't speak to the values for GCRMA, but my suspicion would be that there are slight differences in rounding between the implementations, explaining the differences at the lowest intensity for RMA. However, I can not attest to the correctness or otherwise of the ArrayAssist implementatio ...
written 14.1 years ago by Ben Bolstad1.1k
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Answer: A: LIMMA No residual using rmaPLM
... > > Hello > > I have a general question regarding pre-processing data using RMA. > > Due to memory constraints, I am using the function justRMA() instead of > fitPLM() for pre-processing my data (I have a couple of hundred samples so > far). Is there a way to obtain standard ...
written 14.1 years ago by Ben Bolstad1.1k
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Answer: A: LIMMA No residual using rmaPLM
... Indeed, lmFit when it identifies a PLMset object tries to derive weights using the se.chip.coef slot of the PLMset object. By default rmaPLM does not return these but fitPLM would. Looking back through your previous code it appears as though what you were trying to do is compare situations where yo ...
written 14.1 years ago by Ben Bolstad1.1k
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Answer: A: LIMMA No residual using rmaPLM
... I'd recommend that you use fitPLM rather than rmaPLM for these purposes. The reason why it is giving "reasonable results" in the first case and an error in the other case, is that it is using your user supplied weights in the earlier situation and trying to derive some sensible weights based on the ...
written 14.1 years ago by Ben Bolstad1.1k
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Comment: C: AffyPLM
... Perhaps you could elaborate on what you think the error is with yeast in affyPLM 1.3.3 and won't be in affyPLM 1.4.2? If it is not fixed then I might be able to fix it. Ben On Fri, 22 Jul 2005, lucia Garc?a wrote: > Hi, > I`m interesting in update AffyPLM to version 1.4.2, but it's only t ...
written 14.3 years ago by Ben Bolstad1.1k
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Answer: A: NA and quantile normalization
... If your data initially has NAs then it is quite probable that normalize.quantiles() would introduce additional NA (or more likely turn the entire matrix into NA) since it does not make special allowances for NA values. I think the normalizeQuantiles() function in the limma package handles NA's more ...
written 14.3 years ago by Ben Bolstad1.1k

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