User: lgautier@altern.org

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Posts by lgautier@altern.org

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Comment: C: revmap question
... Hi Herve, That would solve that particular requirement you are having with unlist. (I have one comment, inserted in your proposal below). That could also be the first step toward names-oriented features for vectors. Example: # split on the "names" if no factor specified split2 <- function(x, ...
written 10.4 years ago by lgautier@altern.org950
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Comment: C: revmap question
... > > > lgautier at altern.org wrote: >>> James W. MacDonald wrote: >>>> Hi Raffaele, >>>> >>>> rcaloger wrote: >>>>> Hi, >>>>> I found very interesting the possibility of using reversing the >>>>> mapp ...
written 10.5 years ago by lgautier@altern.org950
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Comment: C: revmap question
... > James W. MacDonald wrote: >> Hi Raffaele, >> >> rcaloger wrote: >>> Hi, >>> I found very interesting the possibility of using reversing the >>> mapping by revmap in the XXXX.db annotation databases. >>> >>> However, I have two prob ...
written 10.5 years ago by lgautier@altern.org950
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Removing probes from AffyBatch
... > Hi Nathan, > > No, I never did get around to making a package for the remove > probes/probe sets functions, mostly because I don't know how! > I just used it again myself, and had to update the code slightly. The code > below works with R 2.7.2. As for how many probes you can re ...
cdf probe biostrings written 10.5 years ago by lgautier@altern.org950
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Comment: C: questions about altcdfenv
... > Hi Hui-Yi, > > See this recent post about another way to remove probe sets: > > https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html > > This will temporarily remove the probe sets from the regular > yeast2cdf, and it's much easier to use than atlcdfenvs i ...
written 10.5 years ago by lgautier@altern.org950
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Comment: C: Using biomaRt to check probe locations
... Section 5 in the main vignette for the 'altcdfenvs' packages shows how to quickly check what probesets of interest are "really" made of. It uses Biostrings, and the code can be edited to suit custom needs. I have written quickly an example with the probeset mentioned (this is going through the refs ...
written 10.6 years ago by lgautier@altern.org950
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heatmap and cdfenv problems
... > Dear BioC list, > > After searching the BioC list and books and googling, I still cannot > figure > out the questions which are described below. Any suggestions will be > really > appreciated. > > 1. I have wt, mut-a, mut-b strains, each of them has 2 replicates. After ...
annotation go yeast2 cdf heatplus written 10.6 years ago by lgautier@altern.org950
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Answer: A: CDF properties
... Check: http://thread.gmane.org/gmane.science.biology.informatics.conductor/14 854 > Hello members > I have a custom chip where one probe often belongs in multiple probe > sets. > To that end I want to know if the "one probe in one probeset only or > in multiple probesets" paramet ...
written 10.8 years ago by lgautier@altern.org950
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Comment: C: makecdfenv and multi-mapping probes on Mouse Gene 1.0 ST array
... > On Sun, May 11, 2008 at 10:38 AM, Heidi Dvinge wrote: >> On 11 May 2008, at 14:28, Sean Davis wrote: >>> On Sun, May 11, 2008 at 8:01 AM, Heidi Dvinge wrote: >>>> Dear all, >>>> I'm currently looking at some Mouse Gene 1.0 ST arrays, and have used the m ...
written 10.9 years ago by lgautier@altern.org950
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Comment: C: LumiBatch: problem when renaming samples
... > Unfortunately the data are confidential so I can not send an example. If the output of "sessionInfo()" on your end, as well as a copy/paste of the error message thrown by R, are classified it is harder for people to try providing help. > Actually, the problem is in the summarization. Both ...
written 10.9 years ago by lgautier@altern.org950

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