Question: Select function not working in R; how to correct custom select
0
gravatar for ekl
11 days ago by
ekl0
ekl0 wrote:

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"

ADD COMMENTlink modified 11 days ago by James W. MacDonald51k • written 11 days ago by ekl0
Answer: Select function not working in R; how to correct custom select
0
gravatar for James W. MacDonald
11 days ago by
United States
James W. MacDonald51k wrote:

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

ADD COMMENTlink written 11 days ago by James W. MacDonald51k

Okay, then how do I add feature data in order to find differentially expressed genes?

ADD REPLYlink written 7 days ago by ekl0

Your question doesn't make sense to me. I just showed you how to get the annotation data, and having the annotation data does nothing for finding differentially expressed genes. If you are asking how to put the data in the featureData slot, then read the help page for eSet or perhaps ExpressionSet. If you are asking how to find differentially expressed genes, read the limma User's Guide.

ADD REPLYlink written 7 days ago by James W. MacDonald51k
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