User: Mayte Suarez-Farinas
Mayte Suarez-Farinas • 510
- Reputation:
- 510
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- United States
- Last seen:
- 4 years, 7 months ago
- Joined:
- 12 years, 9 months ago
- Email:
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Posts by Mayte Suarez-Farinas
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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 4.6 years ago by
Mayte Suarez-Farinas • 510
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... 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 ...
written 5.7 years ago by
Mayte Suarez-Farinas • 510
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... 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 5.9 years ago by
Mayte Suarez-Farinas • 510
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... 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 ...
written 5.9 years ago by
Mayte Suarez-Farinas • 510
• updated
5.9 years ago by
James W. MacDonald ♦ 52k
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... 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 6.2 years ago by
Mayte Suarez-Farinas • 510
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... 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 6.2 years ago by
Mayte Suarez-Farinas • 510
0
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2
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...
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 6.2 years ago by
Mayte Suarez-Farinas • 510
0
votes
2
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2.5k
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2
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... 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 ...
written 6.2 years ago by
Mayte Suarez-Farinas • 510
• updated
6.2 years ago by
James W. MacDonald ♦ 52k
0
votes
1
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704
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1
answer
... 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 ...
written 7.1 years ago by
Mayte Suarez-Farinas • 510
• updated
7.1 years ago by
delhomme@embl.de • 1.2k
0
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1
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668
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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 7.6 years ago by
Mayte Suarez-Farinas • 510
Latest awards to Mayte Suarez-Farinas
Popular Question
4.6 years ago,
created a question with more than 1,000 views.
For problem while loading affycoretools
Popular Question
4.6 years ago,
created a question with more than 1,000 views.
For annotation of a probe in hgu133plus2
Popular Question
4.6 years ago,
created a question with more than 1,000 views.
For problem while loading affycoretools
Popular Question
4.6 years ago,
created a question with more than 1,000 views.
For problem while loading affycoretools
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