User: Nianhua Li
Nianhua Li • 870
- Reputation:
- 870
- Status:
- Trusted
- Location:
- Last seen:
- 12 years, 2 months ago
- Joined:
- 13 years, 6 months ago
- Email:
- n**@fhcrc.org
0
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Answer:
A: Annotation of U95av2 array
... Hi, James and George,
The source data that we used for building the current hgu95av2 package
in bioc
2.0 was downloaded on Feb 28, 2007. Hs.443948 was linked with 3576 in
the source
data. Unfortunately, it is too late to update the packages at this
time.
The way it works is that we download all th ...
written 12.3 years ago by
Nianhua Li • 870
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4
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Answer:
A: homology package question
... Hi, James,
The source file of mmuhomology is
ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/hmlg.ftp (download on
02/28/2007)
and the description is
ftp://ftp.ncbi.nih.gov/pub/HomoloGene/README-old
According to the description, the 4th and 7th column of hmlg.ftp are
Entrez Gene
ID, the 5th and 8th ...
written 12.3 years ago by
Nianhua Li • 870
0
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2
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Answer:
A: hyperGTest, KEGG
... Hi, Ivan,
library(KEGG, lib="~/annoprep/bin-13")
x <- c("04360", "05214", "01030")
## Assume Hu19K8Build17102006 is the annotation for human genes,
## you prefix the KEGG ID with human KEGG pathway code "hsa"
x <- paste("hsa", x, sep="")
g <- mget(x, KEGGPATHID2EXTID)
## then maybe you wan ...
written 12.4 years ago by
Nianhua Li • 870
0
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2
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... Hi, Gregory,
The package hgu133plus2 is maintained by our team at the Department of
computational biology at Fred Hutchinson Cancer Research Center at
Seattle, WA.
We are part of the biocore team (i.e. the core team of bioconductor).
The
package is updated once every six months by using another R p ...
written 12.4 years ago by
Nianhua Li • 870
0
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1
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495
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1
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... Hi, Asta,
> So my package is built 7 days after the official packet.
Even though the package was "published" on Marth 15, the source data
was downloaded from public data resources on Feb 28. So the
differences in source data are about 3 weeks.
> I use the public representative id from rat23 ...
written 12.4 years ago by
Nianhua Li • 870
0
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0
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... Dear Tae-Hoon,
Thanks for the bug report. KEGG changed their FTP site structure on
March 31. I
have updated AnnBuilder. The lastest version is 1.13.23 which is
available at
svn repository now. You can get it via biocLite tomorrow.
thanks
nianhua
...
written 12.4 years ago by
Nianhua Li • 870
0
votes
2
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5.9k
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2
answers
Answer:
A: AnnBuilder GO url question
... Hi, Tae-Hoon,
Even if accessing GO website is a problem, it won't affect your custom
annotation package. There are only 3 objects in the custom package
that are
related to GO: GO, GO2PROBE and GO2ALLPROBES. Here I
use to
represent your package name. GO and GO2PROBE are created by
using
direct mapp ...
written 12.4 years ago by
Nianhua Li • 870
0
votes
1
answer
227
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1
answers
... Hi,
Isn't it a solved issue?!
http://thread.gmane.org/gmane.science.biology.informatics.conductor/11
908/focus=11926
The latest version is 1.15.12.
nianhua
...
written 12.4 years ago by
Nianhua Li • 870
0
votes
1
answer
119
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1
answers
Answer:
A: Pathways missing
... Hi, Mayte,
The hgu133a2 you are using is the most updated version in
bioconductor, but the
source data that we used to build this package was download in Aug,
2006. There
will be more updated data packages (source and windows binaries)
available
before next Thursday (actually maybe this Thursday). ...
written 12.5 years ago by
Nianhua Li • 870
0
votes
1
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362
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1
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Comment:
C: ABPkgBuilder trouble
... Hi, Johan,
A couple of questions/suggestions and one offer:
1. You mentioned that you have tried AnnBuilder on two windows
computers. Could you try just the perl script I sent to you in my last
email and tell me the result?
2. Did you see the perl warning about locale warning when you ran the
per ...
written 12.5 years ago by
Nianhua Li • 870
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