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Question: Celegans.db_2.3.5: Wormbase version
0
gravatar for Julie Zhu
8.5 years ago by
Julie Zhu3.9k
United States
Julie Zhu3.9k wrote:
Hi, I used celegans.db_2.3.5 to convert affy ID to WormBaseID. Could you please let me know the version of wormbase (e.g. WS180, WS200, etc..) that was used for celegans.db_2.3.5? Thank you very much for your help! Kind regards, Julie
celegans affy convert • 256 views
ADD COMMENTlink modified 8.5 years ago by Marc Carlson7.2k • written 8.5 years ago by Julie Zhu3.9k
Answer: Celegans.db_2.3.5: Wormbase version
0
gravatar for Marc Carlson
8.5 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Julie, Unfortunately, the 2.3.5 packages are old enough that we were not yet stamping that information into the manual pages. I can tell you that it was built with what was the most recent version for celegans that UCSC had "at that time", and that the vintage means that this package was built around this time one year ago. So if you really need to track it down, you might be able to get that information from UCSC. But a better option is to use more current annotation packages. If you are willing to upgrade to the latest version (released just last spring), then you will notice that the data about what build was used has been improved to be much more specific.: So for 2.4.1, if you look at the manual page for a mapping that is impacted by UCSC data you will notice that it is much more specific now. So: ?celegansCHRLOC will show that it was built with: ftp://hgdownload.cse.ucsc.edu/goldenPath/ce6 Hope this helps you, Marc On 09/02/2010 01:57 PM, Zhu, Julie wrote: > Hi, > > I used celegans.db_2.3.5 to convert affy ID to WormBaseID. Could you please > let me know the version of wormbase (e.g. WS180, WS200, etc..) that was used > for celegans.db_2.3.5? > > Thank you very much for your help! > > Kind regards, > > Julie > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 8.5 years ago by Marc Carlson7.2k
Hi Marc, Thank you very much for the quick response and detailed explanation! We used the package last year. The paper is almost ready to be submitted, so we will most likely keep the annotation as it is. According to http://hgdownload.cse.ucsc.edu/downloads.html#c_elegans, it was updated to ce6 on May 2008. Thanks again for your help! Kind regards, Julie On 9/2/10 8:13 PM, "Marc Carlson" <mcarlson at="" fhcrc.org=""> wrote: > Hi Julie, > > Unfortunately, the 2.3.5 packages are old enough that we were not yet > stamping that information into the manual pages. I can tell you that it > was built with what was the most recent version for celegans that UCSC > had "at that time", and that the vintage means that this package was > built around this time one year ago. So if you really need to track it > down, you might be able to get that information from UCSC. > > But a better option is to use more current annotation packages. If you > are willing to upgrade to the latest version (released just last > spring), then you will notice that the data about what build was used > has been improved to be much more specific.: > > So for 2.4.1, if you look at the manual page for a mapping that is > impacted by UCSC data you will notice that it is much more specific > now. So: > > ?celegansCHRLOC > > will show that it was built with: > > ftp://hgdownload.cse.ucsc.edu/goldenPath/ce6 > > > Hope this helps you, > > > Marc > > > > On 09/02/2010 01:57 PM, Zhu, Julie wrote: >> Hi, >> >> I used celegans.db_2.3.5 to convert affy ID to WormBaseID. Could you please >> let me know the version of wormbase (e.g. WS180, WS200, etc..) that was used >> for celegans.db_2.3.5? >> >> Thank you very much for your help! >> >> Kind regards, >> >> Julie >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 8.5 years ago by Julie Zhu3.9k
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