User: Ramon Diaz

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Ramon Diaz1.1k
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Posts by Ramon Diaz

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Answer: A: Parallel Computing of varSelRF and tuneRF
... Dear Min, (I was on vacation, and thus the delay). You are asking about different packages and functions. Regarding the varSelRF package, some of the functions are parallelized, as documented in the help. See, for instance, varSelRFBoot, and its arguments "usingCluster" and "TheCluster". Best, R ...
written 8.9 years ago by Ramon Diaz1.1k
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Comment: C: "romer"ing and "roast"ing around gene sets
... Dear Gordon, Thanks a lot for your answer. It clarifies all the issues. And, of course, thanks for such a nice piece of software. Best, R. On Monday 19 July 2010 01:57:21 Gordon K Smyth wrote: > Dear Ramon, > > I agree. Using roast() on a database on gene sets is fine as long as you & ...
written 9.0 years ago by Ramon Diaz1.1k
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Comment: C: "romer"ing and "roast"ing around gene sets
... Dear Gordon, Reading your email, I think there is something I am not following completely. You say, regarding the GSEA-like approach in "romer" > This is actually a > biologically well-motivated approach when you are testing large numbers of > sets. > > If you want to test every set ...
written 9.0 years ago by Ramon Diaz1.1k
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Answer: A: Copy number variation
... Dear Kay, You might want to look at CNVassoc. The method is described here Gonzalez J, Subirana I, Escaramis G, Peraza S, Caceres A, Estivill X, Armengol L. Accounting for uncertainty when assessing association between copy number and disease: a latent class model. BMC Bioinformatics 2009; 10:172+ ...
written 9.2 years ago by Ramon Diaz1.1k
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Answer: A: missing values in limma/contrasts.fit
... Dear Albyn, On Monday 14 December 2009 20:15:05 Albyn Jones wrote: > Dear BioConductor Folk > > The help file for contrasts.fit states: > > "Warning. For efficiency reasons, this function does not > re-factorize the design matrix for each probe. A consequence is > ...
written 9.6 years ago by Ramon Diaz1.1k
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Comment: C: failure to install: aCGH depends on unavailable package
... Dear Patrick, Thanks a lot! Best, R. On Friday 25 September 2009 19:10:03 Patrick Aboyoun wrote: > Ramon, > I am not sure what happened to the sma package on CRAN. It must have > been removed from the repository over the past week since our build > system had fresh installations la ...
written 9.8 years ago by Ramon Diaz1.1k
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failure to install: aCGH depends on unavailable package
... Dear All, I just noticed (failures installing a bunch of BioC packages in new R installations) that aCGH depends on "sma", but sma is no longer available. Thus, the recommended procedure source("http://bioconductor.org/biocLite.R") biocLite("aCGH") will fail. And any package which depends on aCGH ...
acgh cancer written 9.8 years ago by Ramon Diaz1.1k • updated 9.8 years ago by Patrick Aboyoun1.6k
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Comment: C: snapCGH fails in runBioHMM
... Dear John, Thanks a lot! Best, R. On Tuesday 12 May 2009 17:53:40 J-C. Marioni wrote: > Dear Ramon, > > Sorry about the delay in responding to your messages - I was away last > week. I suspect that some of the problems are due to the Namespace - I'll > work on this today and uplo ...
written 10.2 years ago by Ramon Diaz1.1k
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Comment: C: snapCGH fails in runBioHMM
... Dear Wolfgang, On Tuesday 12 May 2009 16:52:30 Wolfgang Raffelsberger wrote: > Hi Ramon, > > just to say that I posted another message concerning an error with > snapCGH package on this list on may 4th, but got no reply. Yes, I am expecting something similar. For my own particualr prob ...
written 10.2 years ago by Ramon Diaz1.1k
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snapCGH fails in runBioHMM
... Dear All, snapCGH (v. 1.12 in BioC 2.4 for sure; most likely v. 1.13 in BioC 2.5 too) fails with the error C symbol name "runNelderMead" not in DLL for package "snapCGH" The problem is that the NAMESPACE file is not loading the required code. Sure enough, if one loads the .so file manually (e.g., ...
acgh microarray twochannel cancer limma snapcgh written 10.2 years ago by Ramon Diaz1.1k • updated 10.2 years ago by Wolfgang Raffelsberger160

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