User: Laurent Gautier

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Laurent Gautier2.2k
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Posts by Laurent Gautier

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HTqPCR and Biobase's eSet
... Hi Heidi, I am currently looking iwith interest at your package HTqPCR and I have the following question and suggestion. The class "qPCRset" is really looking like a sort of "eSet" (defined in Biobase), just without "phenoData" or "assayData". Would it make sense to get qPCRset to inherit from "eS ...
biobase htqpcr written 6.0 years ago by Laurent Gautier2.2k • updated 6.0 years ago by james perkins300
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Comment: C: normalization one color microarrays
... On 2011-08-24 23:04, Sean Davis wrote: > On Wed, Aug 24, 2011 at 4:08 PM, Paz Tapia Ramirez > wrote: >> >> >> >> >> >> >> >> >> Hello, I am starting to work with ONE color microarrays from Agilent, and I read that during the pre-processin ...
written 6.2 years ago by Laurent Gautier2.2k
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Answer: A: Question about quantile normalization
... On 2011-08-01 06:55, qwertyui_period at yahoo.co.jp wrote: > Dear all, > > My environment is limma Version 3.2.2, R version 2.10.1, and Windows XP. > I'm going to normalize the microarray data by "normalizeBetweenArrays" > which is the quantile normalization function in "limma" packag ...
written 6.3 years ago by Laurent Gautier2.2k
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Answer: A: about limma
... I do not think that there is any technical limitation that would prevent you from using it with "non log-transformed data". However, note that if working on microarray data homoscedasity might be very far from respected and this place the post-fit part of the analysis pipeline (eBayes or treat) on u ...
written 6.4 years ago by Laurent Gautier2.2k
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Answer: A: Re-annotation of probes for an Affy custom microarray
... Hi, The package altcdfenvs was written for such use-cases. Best, L. On 2011-06-21 01:19, Ariel Grostern wrote: > Hello, > > I have a custom Affy Genechip that was designed using a draft version of a bacterial genome. We now have the finished version of the genome sequence available, so ...
written 6.4 years ago by Laurent Gautier2.2k
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Comment: C: Bimap and flatten()
... Hi Marc, Thanks for the answer. Since the documentation for the class Bimap is likely the first place one facing an instance would reach when looking for more information, would it make sense to mention that toTable() should be used where flatten() is described (as not much suggests that flatten() ...
written 6.6 years ago by Laurent Gautier2.2k
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Bimap and flatten()
... Hi, The documentation for Bimap (in AnnotationDbi) refers to a generic "flatten()" that does not appear to be exported. Is this by design or is this an oversight ? Thanks, Laurent ...
written 6.6 years ago by Laurent Gautier2.2k • updated 6.6 years ago by Marc Carlson7.2k
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Comment: C: org.*.eg.db problem
... Even shorter, one could use the "::" operator and write org.Mm.eg.db::egCHRLOC. The presumed issue is more that one could import (attach) several org.X.eg.db packages, still write egCHRLOC and get something dependent on the order in which the import was made (hence the note about implementing the p ...
written 7.0 years ago by Laurent Gautier2.2k
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Comment: C: org.*.eg.db problem
... On 01/12/10 17:50, Martin Morgan wrote: > On 12/01/2010 08:48 AM, arne.mueller at novartis.com wrote: >> Hello, >> >> the org.*.eg.db environments cannot be used in a generic way :-( . Let's >> say I'm writing a function that needs an entire org.*.eg.db environment as > ...
written 7.0 years ago by Laurent Gautier2.2k
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Answer: A: Nimblegen Arrays and Ringo
... The NimbleGen image analysis software can output the results to different formats (pairs, xys, ...), all containing slightly different information for a given hybridization. The NDF is the most complete description for the probes on a given array, and there is no need to repeat that information in ...
written 7.0 years ago by Laurent Gautier2.2k

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