User: Laurent Gautier

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Laurent Gautier2.2k
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Posts by Laurent Gautier

<prev • 224 results • page 2 of 23 • next >
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Answer: A: error msg for probe match (altcdfenvs)
... On 28/10/10 23:48, Jack Luo wrote: > Hi, > > I am new to the probe match package altcdfenvs, when I was trying the code > from the link: > > http://127.0.0.1:21417/library/altcdfenvs/html/matchAffyProbes.html > > library(hgu133aprobe) > > filename<- system.file("exam ...
written 8.9 years ago by Laurent Gautier2.2k
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Answer: A: dynamic range/scale using exprs (Biobase)
... On 06/08/10 00:32, Lucia Peixoto wrote: > (...) > although that only gives me the average expression values. > Is the data extracted by "exprs" already in log2 scale? can someone tell why > I am seeing such difference in scale/dynamic range? Am I not using "exprs" > correctly? > &g ...
written 9.1 years ago by Laurent Gautier2.2k
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Comment: C: package pair "hugene10stv1cdf"/"hugene10stprobeset.db"
... Hi Benilton, Thanks for the information. I did miss the named argument "target" at the end of the signature for rma(). However, one note about the documentation: now that know the existence of "target" I am still unable to infer from the help file for rma() that target="core" returns "transcript c ...
written 9.4 years ago by Laurent Gautier2.2k
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Comment: C: package pair "hugene10stv1cdf"/"hugene10stprobeset.db"
... Hi Marc, Affymetrix possibly changing the way features are described might not be the only source of confusion. Using "oligo" does not appear to make things must better, as the information that can be obtained after running "rma()" is: > eset at annotation [1] "pd.hugene.1.0.st.v1" Is this t ...
written 9.4 years ago by Laurent Gautier2.2k
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Comment: C: package pair "hugene10stv1cdf"/"hugene10stprobeset.db"
... Hi Marc, What I am reading translates into very little confidence in anything related to hugene 1.0ST in the bioconductor "affy" pipeline, and I really think that it should be more difficult to use it without going through steps that require one to explicitly see that this is untested/not recommend ...
written 9.4 years ago by Laurent Gautier2.2k
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Comment: C: package pair "hugene10stv1cdf"/"hugene10stprobeset.db"
... Hi James, Thanks for the clarifications. I am happy to see that Affymetrix has picked up the concept of alternative CDF definitions and makes it easier for its users. Regarding bioconductor, wouldn't it make sense to either mark packages as "unsupported", or better take them to a different locatio ...
written 9.4 years ago by Laurent Gautier2.2k
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package pair "hugene10stv1cdf"/"hugene10stprobeset.db"
... Dear List, I am noting potential issues in the package pair "hugene10stv1cdf"/"hugene10stprobeset.db", as the respective sets of probe set IDs are not overlapping: > library(hugene10stv1cdf) > library(hugene10stprobeset.db) > summary(ls(hugene10stv1cdf) %in% Lkeys(hugene10stprobesetSYM ...
annotation cdf written 9.4 years ago by Laurent Gautier2.2k • updated 9.4 years ago by James W. MacDonald51k
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Answer: A: pair information of microRNA and Targets prediction
... Hi Weihsin, My understanding is that microRNA only contains example data (so the exact version for the data source is of moderate importance). The only package containing database data might be "RmiR.Hs.miRNA" (dependency of RmiR). The version might be indicated in the source code (check the SVN re ...
written 9.6 years ago by Laurent Gautier2.2k
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13 bioinformatics and bioinformatics-related positions
... Dear List, There are 13 bioinformatics and bioinformatics-related positions at CBS, Department of Systems Biology - Technical University of Denmark, located in the Copenhagen area. A description of the positions, as well as a link to an online application form, can be found at: http://www.dtu.dk/ ...
written 9.6 years ago by Laurent Gautier2.2k
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Scerevisiaetilingprobe appears to be missing from Bioconductor repositories ?
... Dear List, We are facing an issue when trying to follow the vignette assessNorm for the package davidTiling. The required package Scerevisiaetilingprobe appears to be missing from Bioconductor repositories. > biocLite("Scerevisiaetilingprobe") Using R version 2.10.0, biocinstall version 2.5 ...
written 9.8 years ago by Laurent Gautier2.2k • updated 9.8 years ago by Wolfgang Huber13k

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