hyperGTest and ath1121501-continued

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Tine Casneuf ▴ 80

@tine-casneuf-1773

Last seen 10.3 years ago

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 work with the AGI-IDs and not the entrezIDs): > hgOver <- hyperGTest(params) Error in get(x, envir, mode, inherits) : variable "ath1121501ENTREZID" of mode "environment" was not found Did I completely miss it and is there a way around this problem or should I look for another function, like Thomas Girke's GOHyperGAll? Many thanks in advance, Tine

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ADD COMMENT • link updated 18.2 years ago by Nianhua Li ▴ 870 • written 18.2 years ago by Tine Casneuf ▴ 80

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Nianhua Li ▴ 870

@nianhua-li-1606

Last seen 10.3 years ago

Dear Tine, Could you please run traceback() and sessionInfo() after the error and send me the results? Many thanks. Those will be helpful in debugging. It will be even better if you happen to have a small example script. thanks nianhua

ADD COMMENT • link 18.2 years ago Nianhua Li ▴ 870

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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 identical to ath1121501ACCNUM? I have build my own cdf and annotation package for this array, is the following correct: > Myath1annotENTREZID <- Myath1annotACCNUM in order to being able to use hyperGTest? thanks! Nianhua Li wrote: >Dear Tine, > >Could you please run traceback() and sessionInfo() after the error and send me >the results? Many thanks. Those will be helpful in debugging. It will be even >better if you happen to have a small example script. > >thanks > >nianhua > >_______________________________________________ >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 REPLY • link 18.2 years ago Tine Casneuf ▴ 80

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Dear Tine, > I am still wondering about the following: the variable > ath1121501ENTREZID is not defined in the ath1121501 environment, right? ath1121501ENTREZID is defined in the ath1121501 environment, but it is a reference to ath1121501ACCNUM. > Is in this case (for this arabidopsis-specific environment only) > ath1121501ENTREZID identical to ath1121501ACCNUM? Yes. > > I have build my own cdf and annotation package for this array, is the > following correct: > > > Myath1annotENTREZID <- Myath1annotACCNUM > > > in order to being able to use hyperGTest? Yes if your annotation package was built by athPkgBuilder. best nianhua

ADD REPLY • link 18.2 years ago Nianhua Li ▴ 870

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