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!!!

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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