[BioC] yeast2 package deprecation

[James W. MacDonald]

Hi Hui-Yi,

Hui-Yi Chu wrote:
> Hi everyone in list,
> 
> I tried to use limma2annaffy function in "affycoretools" package, but got
> the message as following, can anybody tell me how to solve it? Thank you in
> advance!!!

Yes.

For now, let's say your ExpressionSet is called 'eset'.

annotation(eset) <- "yeast2.db"

Then run the analysis as usual.

Best,

Jim


> 
> Hui-Yi
> 
> 
> 
> Do you want to accept or change these values? [ a/c ]a
> Loading required package: yeast2
> 
> ******* Deprecation warning *******:
> 
> The package 'yeast2' is deprecated and will not be supported in the future.
> 
> Instead we strongly reccomend that you should start using the 'yeast2.db'
> package.
> 
> We hope you will enjoy these new packages.  If you still have questions, you
> can search
> (http://dir.gmane.org/gmane.science.biology.informatics.conductor) or ask
> the mailing list
> (http://bioconductor.org/docs/mailList.html).
> 
> 
> Error in do.call(paste(chip, "_dbconn", sep = ""), list()) :
>   could not find function "yeast2_dbconn"
> In addition: Warning message:
> In chkPkgs(chip) :
>   The yeast2 package does not appear to contain annotation data.
> 
> 
> 
> #####
> R version 2.7.2 (2008-08-25)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
> 
> other attached packages:
>  [1] yeast2_2.2.0         affycoretools_1.12.1 annaffy_1.12.1
>  [4] KEGG.db_2.2.0        gcrma_2.12.1         matchprobes_1.12.1
>  [7] biomaRt_1.14.1       RCurl_0.9-3          GOstats_2.6.0
> [10] Category_2.6.0       RBGL_1.16.0          annotate_1.18.0
> [13] xtable_1.5-3         GO.db_2.2.0          AnnotationDbi_1.2.2
> [16] RSQLite_0.7-0        DBI_0.2-4            graph_1.18.1
> [19] gplots_2.6.0         gdata_2.4.2          gtools_2.5.0
> [22] Heatplus_1.10.0      RColorBrewer_1.0-2   genefilter_1.20.0
> [25] survival_2.34-1      yeast2cdf_2.2.0      limma_2.14.6
> [28] affy_1.18.2          preprocessCore_1.2.1 affyio_1.8.1
> [31] Biobase_2.0.1
> 
> loaded via a namespace (and not attached):
> [1] cluster_1.11.11 XML_1.94-0.1
> 
> 
> Thanks again!!
> Hui-Yi
> 
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662