Question

Arabidopsis thaliana cdf ath1121501

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Naira Naouar ▴ 140

@naira-naouar-2394

Last seen 10.2 years ago

Dear all, I would like to ensure that ath1121501cdf is based on TAIR6? If this is the case, when should we expect the next release with TAIR7 annotation? Thanks, Naira -- ================================================================== Naira Naouar Tel:+32 (0)9 331 38 25 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM nanao at psb.ugent.be http://www.psb.ugent.be

cdf cdf • 980 views

ADD COMMENT • link updated 17.1 years ago by James W. MacDonald 67k • written 17.2 years ago by Naira Naouar ▴ 140

score 0 · Answer 1 · 2007-09-25

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 8 hours ago

United States

Hi Naira, Do you perhaps mean the ath112501 package? The cdf package you mention is based solely on the cdf that is supplied by Affy. Best, Jim Naira Naouar wrote: > Dear all, > > I would like to ensure that ath1121501cdf is based on TAIR6? > If this is the case, when should we expect the next release with TAIR7 > annotation? > > Thanks, > Naira >

ADD COMMENT • link 17.1 years ago James W. MacDonald 67k

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Hi James, Sorry I was not clear in my previous mail. You are right I meant the ath1121501 package. For the AGI locus identifiers (ex: AT2G35060) that are linked to the affymetrix "_at" codes in ath1121501ACCNUM, I would like to know if you used TAIR6 (or TAIR7) or an other source. > library(ath1121501) > get("267423_at", ath1121501ACCNUM) [1] "AT2G35060" Thanks, Naira James W. MacDonald wrote: > Hi Naira, > > Do you perhaps mean the ath112501 package? The cdf package you mention > is based solely on the cdf that is supplied by Affy. > > Best, > > Jim > > > > Naira Naouar wrote: >> Dear all, >> >> I would like to ensure that ath1121501cdf is based on TAIR6? >> If this is the case, when should we expect the next release with >> TAIR7 annotation? >> >> Thanks, >> Naira >> -- ================================================================== Naira Naouar Tel:+32 (0)9 331 38 25 fax:+32 (0)9 3313863 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM nanao at psb.ugent.be http://www.psb.ugent.be

ADD REPLY • link 17.1 years ago Naira Naouar ▴ 140

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Quoting Naira Naouar <nanao at="" psb.ugent.be="">: > Hi James, > > Sorry I was not clear in my previous mail. You are right I meant the > ath1121501 package. > > For the AGI locus identifiers (ex: AT2G35060) that are linked to the > affymetrix "_at" codes in ath1121501ACCNUM, I would like to know if you > used TAIR6 (or TAIR7) or an other source. > > > library(ath1121501) > > get("267423_at", ath1121501ACCNUM) > [1] "AT2G35060" > > > Thanks, > Naira > The very latest version of that package is in devel right now and should go into release on October the 5th. That release is based on data that was downloaded from TAIR on August the 29th and corresponds to their build dated the 2nd of August. According the the TAIR website, they switched to TAIR7 on the 3rd of July. http://www.arabidopsis.org/biocyc/releasenotes.jsp So in short a TAIR7 version of ath1121501 is available right now if you want to use the devel branch. And this package will see wide release on the 5th of October. Marc

ADD REPLY • link 17.1 years ago Marc Carlson ★ 7.2k