User: Ben Bolstad

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Ben Bolstad1.2k
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Posts by Ben Bolstad

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Comment: C: oligo: crash/segfault when fitting probelevel model
... Also it might be possible to turn threading off in OpenBLAS rather than just recompiling R. See https://github.com/xianyi/OpenBLAS/wiki/faq#multi-threaded     ...
written 12 weeks ago by Ben Bolstad1.2k
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Comment: C: oligo: crash/segfault when fitting probelevel model
... It is debatable as to how far gone over the edge I am :) But it is true that my activity level has been minimal for some years now. In any case preprocessCore does have and has long had it's own pthreads based multithreading implementation. You can control the number of threads it is using with a s ...
written 12 weeks ago by Ben Bolstad1.2k
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Comment: C: Question about quantile normalization and NA value
... At least for the example matrix below, you?ll find the preprocessCore normalize.quantiles() function will generate you the same result as below from limma. Though I make no claims that it is identical in other cases, nor that its treatment of NA is better than any other implementations. Best, Ben ...
written 3.8 years ago by Ben Bolstad1.2k
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Answer: A: rhdf5 segfault
... You might try changing your stack size limits in your shell, before launching R. e.g. ulimit -s unlimited I know I encountered a similar issue with rhdf5 not to long ago reading from a file with a fairly large number of strings, and that was a suitable work around. Note within R Cstack_info() wil ...
written 3.9 years ago by Ben Bolstad1.2k
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Answer: A: segfault ReadAffy cause 'memory not mapped'
... Those changes should be part of the most recent BioC release. Please let me know if you still discover any issues. Ben On Oct 23, 2013, at 7:07 AM, "Brian D. Peyser PhD" wrote: > Below is some previous info on this issue; Dr Bolstad, did you issue a > patch to affyio? > > I had jus ...
written 4.1 years ago by Ben Bolstad1.2k
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Answer: A: AffyPLM
... Please see Brettschneider J, Collin F, Bolstad BM, and Speed TP Quality assessment for short oligonucleotide arrays (with 5 commentaries and rejoinder) Technometrics, 50(3): 241-264 (article), 279-283 (rejoinder), Aug 2008 > Dear Sir, Madam, > > > I'm trying to find a published rep ...
written 4.1 years ago by Ben Bolstad1.2k
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Comment: C: segfault ReadAffy cause 'memory not mapped'
... Well, internally read_abatch is using allocMatrix() to actually allocate the main block of memory that will be used to store the probe intensities. However, there are a lot of places where "int" is used as the indexing variable. Probably if I had had better foresight when I wrote this code 10 year ...
written 4.3 years ago by Ben Bolstad1.2k
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Answer: A: log transform in RMA normalization
... the log transformation occurs at the summarization step. i.e. both background correction and quantile normalization occur on the natural scale. Ben On Jan 24, 2013, at 6:43 AM, Jack Luo wrote: > I am trying to understand the details of the RMA algorithm in terms of log > transform. The pr ...
written 4.8 years ago by Ben Bolstad1.2k
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Answer: A: R 2.15.1 ReadAffy error
... Multichannel Calvin CEL files can be read using affyio::read.celfile() Based on the sessionInfo() I'm guessing the OP is trying to use ReadAffy() from the affy package which would not be appropriate for a SNP array. However, I don't recall at the current time whether I ever fixed affyio::read.celf ...
written 5.4 years ago by Ben Bolstad1.2k
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Answer: A: Quality Diagnostics of Affy Arrays using PLM
... Hi Grant, I can not reproduce this issue at my end. But my suspicion is that when you put the "add=TRUE" argument into your image() on the PLMset it is expanding this to "add.legend=TRUE". Internally the image() method for the PLMset object uses "layout" in this situation (which will not interact ...
written 5.4 years ago by Ben Bolstad1.2k

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Centurion 3.8 years ago, created 100 posts.

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