User: Daniel Rico

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Daniel Rico110
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Posts by Daniel Rico

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Annotation for Mouse Affy SNP arrays (MOUSEDIVm520650)?
... Dear list, I could not find a "pd.mapping" annotation package to use for the Affymetrix Mouse Diversity Genotyping array (MOUSEDIVm520650). Is someone preparing one? I would like to use CRLMM and VanillaICE with this arrays, but it seems I need an appropriate annotation package for that. Thanks ...
annotation cancer vanillaice crlmm written 8.0 years ago by Daniel Rico110
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Comment: C: ArrayExpress: missing cdf environment!
... Thanks Wolfgang!! It is very nice that the method tries to install the package. As "cdfname" is not shown, it is not clear which package is missing. Maybe the package name could be printed in the error message? Thank you guys for the excelent sofware!! Best, Daniel On Oct 16, 2010, at 5:51 PM ...
written 9.0 years ago by Daniel Rico110
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ArrayExpress: missing cdf environment!
... Dear list, I downloaded a dataset from ArrayExpress using ArrayExpress package, and I get an error when I try to see the object created, or a try to normalize it with rma. I am using a Linux Ubuntu. For some reason, a package installation is tried (related with cdf, I guess) but I am not root... I ...
cancer hgu133a cdf arrayexpress written 9.0 years ago by Daniel Rico110 • updated 9.0 years ago by Wolfgang Huber13k
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Comment: C: CGH analysis without genome positions
... Hi, you really need the chromosome and position where the probes map in the genome. You can user readPositionalInfo function in snapCGH package to get that information from previously parsed Agilent txt files. Check the package vignette. Best, Daniel On Apr 6, 2010, at 7:58 PM, Sean Davis wrot ...
written 9.5 years ago by Daniel Rico110
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DNAcopy
... Hello Anguraj, you can impute missing values before segmentation with preprocessing functions in snapCGH or CGHcall packages. Check their vignettes. Best, Daniel -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Anguraj Sadanandam Sent: Thu 1/28/2010 12:57 PM T ...
acgh impute dnacopy snapcgh cghcall written 9.7 years ago by Daniel Rico110
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local and remote biomaRt problems
... Hello, I am trying to use a local biomaRt . > library(biomaRt) # It works with remote biomart: > mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") Checking attributes ... ok Checking filters ... ok # But not with our local biomart: > listMarts(host="ubio.bioinfo.cnio ...
cancer biomart written 10.1 years ago by Daniel Rico110
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CGHregions error
... Dear list, dear CGHcall developers, I am trying to run CGHregions function (from CGHregions) package with copy number data from 1M arrays. As 1 million probes are a lot, I decided to run CGHregions chromosome by chromosome. I am using a data.frame as input data, with copy numbers -1 (loss), 0 (nor ...
cancer cghcall cghregions written 10.3 years ago by Daniel Rico110
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Answer: A: CGHcall error
... Hi James, Check the new vignette from the latest BioConductor version: now you must create and work with CGHcall objects, as the new version does not support data.frames directly (but there is a function that takes the data.frame with raw data and converts it to the corresponding CGHcall package). ...
written 11.0 years ago by Daniel Rico110
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Comment: C: CGHcall error
... hits=-2.6 tests=BAYES_00 X-USF-Spam-Flag: NO Hi Henrik, Sjoerd Vosse, developer of CGHcall, is having a look at my data. Thanks to both! Daniel Henrik Bengtsson wrote: > On Feb 5, 2008 3:44 AM, Daniel Rico wrote: > >> hits=-2.6 tests=BAYES_00 >> X-USF-Spam-Flag: NO >> &g ...
written 11.7 years ago by Daniel Rico110
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CGHcall error
... hits=-2.6 tests=BAYES_00 X-USF-Spam-Flag: NO Dear List, I am trying to use CGHcall function from CGHcall package, trying to use my own normalized and segmented dataframes (Agilent oligo Human 44A, data normalized with MANOR and segmented with GLAD), buy I get this error: EM algorithm started ... ...
cancer organism manor oligo cghcall bac written 11.7 years ago by Daniel Rico110 • updated 11.7 years ago by Henrik Bengtsson2.4k

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