User: Mayte Suarez-Farinas

gravatar for Mayte Suarez-Farinas
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12 years, 7 months ago
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Posts by Mayte Suarez-Farinas

<prev • 52 results • page 1 of 6 • next >
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Answer: A: Reporting Tools error
...   Hi Laurent. I gave up on this for a while, but will try again. I got a new computer , all new installation from scratch and still I get an error when i try to publish a KEGG result.  keggParams<-new("KEGGHyperGParams", geneIds = DEGi_entrez, universeGeneIds=UnivEntrez,                       ...
written 4.5 years ago by Mayte Suarez-Farinas • 510
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KEGG pathway analysis with ReportingTools
... Dear All, I am successfully using the ReportingTools package to detect over- expressed categories using hypergeometric Test for Gene Ontologies and PFAM follwoing the package vignette. When I tried to do the same using KEGG pathways, the function publish does not work. I am surprise because class P ...
pathways go reportingtools written 5.5 years ago by Mayte Suarez-Farinas • 510
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Comment: C: annotation of a probe in hgu133plus2
... Hi James Thanks for guiding me in the right direction. I am updating my pipeline to accommodate this. My only problem was the line publish(tab, htab, .modifyDF = list(entrezLinks, affyLinks)) gave me a msg error Error in .self$prepare(value, .toHTML = .toHTML, .toDF = .toDF, .modifyDF = .modifyDF, ...
written 5.8 years ago by Mayte Suarez-Farinas • 510
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annotation of a probe in hgu133plus2
... Dear annotation builders I notice that one of my favorite genes DEFB4A is missing from the hgu133plus2.db the NetAffy database says that probeset 207356_at correspond to gene DEFB4A yet getSYMBOL('207356_at','hgu133plus2.db') returns NA. This happen in newer versions of this package, since it has b ...
annotation written 5.8 years ago by Mayte Suarez-Farinas • 510 • updated 5.8 years ago by James W. MacDonald ♦ 51k
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Comment: C: problem while loading affycoretools
... I tried all your advice: reinstall R, change mirror, still biocLite("affycoretools") does not install the package bit automatically and downloading the tgz from bit, the package bit does not compile Mayte Suarez-Farinas Research Assistant Professor Laboratory of Investigative Dermatology Biostatist ...
written 6.1 years ago by Mayte Suarez-Farinas • 510
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Comment: C: problem while loading affycoretools
... Hi James and Dan I installed R from scratch and then run the following two lines: biocLite() (success) biocLite("affycoretools") which, after installing several packages gave me the "error: package ‘AnnotationDbi’ could not be loaded" (see ALL outputs below)' Dan, here is the output of biocin ...
written 6.1 years ago by Mayte Suarez-Farinas • 510
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Comment: C: problem while loading affycoretools
... Dear James, Henrik and Steve I tried biocLite("ff") and got the msg: package ?ff? is not available (for R version 3.0.1) (see below). Then I went ahead and download the tar package form (http://cran.r-project.org/web/packages/ff/index.html) and used R CMD install to install it. However, while load ...
written 6.1 years ago by Mayte Suarez-Farinas • 510
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problem while loading affycoretools
... I updated to the most recent R version. After this brand new installation, I get the following error while loading library affycoretools: library(affycoretools) Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘ff’ Error: packag ...
go written 6.1 years ago by Mayte Suarez-Farinas • 510 • updated 6.1 years ago by James W. MacDonald ♦ 51k
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error in easyRNASeq
... Dear All, I am trying to use the easyRNASeq package with 6 RNAseq samples from mouse. Single end, unstranded protocol, 50bp reads. I followed the vignettes and wrote this short code: library("easyRNASeq") library(Rsamtools) library(DESeq) library(edgeR) library(GenomicRanges) library(parallel) lib ...
rnaseq bsgenome easyrnaseq written 7.0 years ago by Mayte Suarez-Farinas • 510 • updated 7.0 years ago by delhomme@embl.de • 1.2k
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Comment: C: errors in FRMA
... >annotation(object) [1] "hgu133plus2" >new.object<-convertPlatform(object,'hgu133a') Loading required package: hgu133aprobe Loading required package: hgu133plus2probe Attaching package: ?hgu133plus2cdf? The following object(s) are masked from ?package:hgu133acdf?: i2xy, xy2i head ...
written 7.5 years ago by Mayte Suarez-Farinas • 510

Latest awards to Mayte Suarez-Farinas

Popular Question 4.5 years ago, created a question with more than 1,000 views. For problem while loading affycoretools
Popular Question 4.5 years ago, created a question with more than 1,000 views. For annotation of a probe in hgu133plus2
Popular Question 4.5 years ago, created a question with more than 1,000 views. For problem while loading affycoretools
Popular Question 4.5 years ago, created a question with more than 1,000 views. For problem while loading affycoretools
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