User: Daren Tan

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Daren Tan150
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Posts by Daren Tan

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Comment: C: Keep getting warning messages of package 'XYZ' was built under R version 2.8.1
... Please clarify my understanding. When R version 2.8.0 was released, all packages in Bioconductor version 2.3 was built with it. During this period, any installation of packages in bioconductor 2.3 did not give any warnings. With the minor release R version 2.8.1, Bioconductor version 2.3 was rebui ...
written 8.8 years ago by Daren Tan150
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Keep getting warning messages of package 'XYZ' was built under R version 2.8.1
... I just installed another bioconductor package "seqinr". I only noticed the warning message today, and fear that my R or bioconductor is broken. Please give me some assurance it is working fine. I dread to reinstall R and bioconductor again. > library("seqinr") Warning message: package 'seqinr' ...
written 8.8 years ago by Daren Tan150 • updated 8.8 years ago by Vincent J. Carey, Jr.6.2k
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Where to download annotation package for Agilent human CGH 44B
... Does anyone know where to download annotation package for Agilent human CGH 44B. I have an urgent need for it. Please help. Thanks Daren _________________________________________________________________ [[elided Hotmail spam]] ...
annotation cgh written 8.8 years ago by Daren Tan150 • updated 8.8 years ago by Marc Carlson7.2k
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Annotation package for Agilent human CGH 44B
... I am using Agilent human CGH 44B for my research. Searching through http://www.bioconductor.org/packages/2.3/data/annotation/, I can't find the appropriate annotation package. Next, I found at http://rss.a cs.unt.edu/Rdoc/library/AnnBuilder/data/descriptionInfo.txt the following statment, which con ...
annotation cgh homo sapiens written 8.8 years ago by Daren Tan150
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U133 plus 2.0 probesets, what to keep and what to filter.
... >From my understanding of U133 plus 2.0 arrays, all the probesets are not created equally based on the Affy's "Probe Set Extension Nomenclature" from http://www.ohsu.edu/gmsr/amc/amc_technology.html#extensions. I would like to select only those probesets that map uniquely to single gene (can hav ...
written 9.0 years ago by Daren Tan150
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Comment: A: Limma: how to get same output as topTable but for all the genes ?
... Hope this helps others After I sent out the earlier email, realized that there is write.fit. My solution is to modify it such that fit2tablefunction (fit, results = NULL, file, digits = 3, adjust = "none", sep = "\t", ...){ if (!is(fit, "MArrayLM")) stop("fit should be an MArrayLM object") ...
written 9.0 years ago by Daren Tan150 • updated 9 months ago by Gordon Smyth32k
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Comment: C: Using wildcard with BiomaRt:getBM
... Thanks steffen for the assurance. I will try your suggestion. > Date: Tue, 25 Nov 2008 20:56:31 -0800> Subject: Re: [BioC] Using wildcard with BiomaRt:getBM> From: steffen@stat.Berkeley.EDU> To: daren76@hotmail.com> CC: bioconductor@stat.math.ethz.ch> > Hi Daren,> > Wildc ...
written 9.0 years ago by Daren Tan150
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Limma: how to get same output as topTable but for all the genes ?
... Apology this question is very general, and no codes to illustrate. How can I emulate topTable to output all the genes, as topTable is not suitable for outputting all genes. ...
limma toptable written 9.0 years ago by Daren Tan150 • updated 4 months ago by Gordon Smyth32k
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Comment: C: Using GenomeGraphs effectively for generating publication quality pictures
... Thanks steffen, I will try your suggestions. > Date: Tue, 25 Nov 2008 20:51:21 -0800> Subject: Re: [BioC] Using GenomeGraphs effectively for generating publication quality pictures> From: steffen@stat.Berkeley.EDU> To: daren76@hotmail.com> CC: bioconductor@stat.math.ethz.ch> > ...
written 9.0 years ago by Daren Tan150
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Using GenomeGraphs effectively for generating publication quality pictures
... Hi, I am using GenomeGraphs to generate gene structures. My codes are below: A few questions that I have 1) How to include the cytoband information e.g. 4q to the ideogram ? How to label the gene in the cytoband with "IL8" ? 2) What colour is actually used by gene and transcript ? I have created ...
affy biomart ideogram genomegraphs written 9.0 years ago by Daren Tan150 • updated 9.0 years ago by steffen@stat.Berkeley.EDU600

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Popular Question 8.8 years ago, created a question with more than 1,000 views. For Limma: how to get same output as topTable but for all the genes ?

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