I am trying to finish a microarray analysis. I need to select information from the A flavus package to find deferentially expressed genes. Select is not working in Annotation Dbi. How do I create a custom select function so that R recognizes the function? Thank you. cdf=AFLAVUSa520391F (22683 affyids) annotation=aflavusa520391f

library("aflavusa520391fcdf") anno<-select(aflavusa520391fcdf, + keys=(featureNames(eset)), + columns=c("SYMBOL","GENENAME"), + keytype="PROBEID") Error in select(aflavusa520391fcdf, keys = (featureNames(eset)), columns = c("SYMBOL", : could not find function "select"

The cdf package is used to map probes to probesets for when you run rma. It doesn't contain any annotation data. For that you would need to (probably) get the data from GEO:

> library(GEOquery)
> z <- getGEO("GPL8345")
> head(Table(z))
              ID    CLONE_ID
1 1569.m00638_at AFLA_000010
2 1569.m00637_at AFLA_000020
3 1569.m00636_at AFLA_000330
4 1569.m00635_at AFLA_000340
5 1569.m00634_at AFLA_000350
6 1569.m00633_at AFLA_000360
                                                  Description
1                              conserved hypothetical protein
2                        penicillin-binding protein, putative
3 multiple ankyrin repeats single kh domain protein, putative
4                         short-chain dehydrogenase, putative
5               NAD dependent epimerase/dehydratase, putative
6                                        hypothetical protein
                                        GO terms             Interpro SPOT_ID
1                                                                          NA
2                                     GO:0046677            IPR001466      NA
3                                                                          NA
4                                                                          NA
5 GO:0003854  GO:0006694  GO:0006808  GO:0016564 IPR002225, IPR008030      NA
6                                                                          NA