User: Tine Casneuf

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Tine Casneuf80
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Last seen:
13 years ago
Joined:
13 years, 4 months ago
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t*************@ebi.ac.uk

Posts by Tine Casneuf

<prev • 8 results • page 1 of 1 • next >
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Comment: C: hyperGTest and ath1121501-continued
... Hi Nianhua, after updating several packages (ath121501, GO,.. ) it worked fine. I am still wondering about the following: the variable ath1121501ENTREZID is not defined in the ath1121501 environment, right? Is in this case (for this arabidopsis-specific environment only) ath1121501ENTREZID identica ...
written 13.0 years ago by Tine Casneuf80
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hyperGTest and ath1121501-continued
... Dear Nianhua & list, to continue the discussion on the hyperGTest and ath1121501 (https://stat.ethz.ch/pipermail/bioconductor/2006-October/014715.html) . As far as I understood, this function needs the ENTREZID variable of the studied environment, which in this case doesn't exist (~because we w ...
written 13.0 years ago by Tine Casneuf80 • updated 13.0 years ago by Nianhua Li870
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Answer: A: Beginner's Q: Where to start given so many packages?
... Depending on the help you are looking for, you will probably find the 'Bioinformatics and Computational biology solutions using R and Bioconductor' book (http://www.bioconductor.org/pub/docs/mogr/) very usefull. It covers both theoretical background and help with R code. More info regarding both R ...
written 13.2 years ago by Tine Casneuf80
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Answer: A: athPkgBuilder data source :missing probesets
... But to me it is hard to think of a way to choose the 'best' locus that is detected by a probeset. And also if you pick 1 of them, it appears as if only 1 is detected by this probeset, while actually there are more. There are I presume not many cases where a measure from these probesets are useful, s ...
written 13.3 years ago by Tine Casneuf80
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Comment: C: (no subject)
... Hi guys, I agree with Thomas. They have taken over from TIGR last year and are taking care of the annotation (that's why the previous releases of the genome were called TIGRx and the last one is TAIR6). About the ath and eath in kegg: we map probesets to locusIDs and not to the transcripts themsel ...
written 13.3 years ago by Tine Casneuf80
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(no subject)
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20060810/ 4b232209/attachment.pl ...
written 13.3 years ago by Tine Casneuf80 • updated 13.3 years ago by Nianhua Li870
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athPkgBuilder
... Hi, I am trying to use AnnBuilder to build a annotation package for the Arabidopsis ATH1 array. The athPkgBuilder function in AnnBuilder doesn't work properly because one of the files is no longer available from TAIRs ftp server. Of the files that this function looks for: fileExt = list( ...
annotation go annbuilder written 13.3 years ago by Tine Casneuf80 • updated 13.2 years ago by Nianhua Li870
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query gramene from biomaRt package
... Dear all, Has anyone managed to query the gramene database from the biomaRt package or can anyone point me to documentation on it? I would like to search for information on Arabidopsis thaliana which is in the database. Many thanks in advance, Tine ...
arabidopsis thaliana written 13.4 years ago by Tine Casneuf80 • updated 13.4 years ago by sdurinck40

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