Microarray Annotation problems

Question

[aoguspider]

Hi,

I am a new user of R. I have been trying to use R to analyze my microarray. I am trying to use the AnnotationDbi package for the annotation, and I have got a problem.

Please see the code as follows:

library(AnnotationDbi)
require(mogene10sttranscriptcluster.db)
tbl=topTable(eset,number=nrow(eset),coef=1)
ids=rownames(tbl)
ids=as.character(ids) #the annotation will only recognize the probeID as characters.
columns(mogene10sttranscriptcluster.db)
keytypes(mogene10sttranscriptcluster.db)
anno1=select(mogene10sttranscriptcluster.db,ids,columns=c('ENTREZID','GENENAME'),keytype='PROBEID')
head(anno1)

And the results comes as follows,

  PROBEID  ENTREZID                          GENENAME
1 10598069     17721      NADH dehydrogenase subunit 5
2 10598069     17711                      cytochrome b
3 10496438     11522 alcohol dehydrogenase 1 (class I)
4 10560624     11816                  apolipoprotein E
5 10608690 100861531             45S pre-ribosomal RNA
6 10608690    236598                 28S ribosomal RNA

I have noticed the same probeID (like 10598069 or 10608690) comes out with two different genes! Why is that happening... Should I trust my analysis results?

Answer 1

[alolex]

Microarray probes do not always map to a single unique gene, some can cross hybridize to multiple genes. You need to research the microarray brand you are analyzing to get a list of all the probes that can potentially cross hybridize to multiple genes and to which genes those are. For example, any Affymetrix probe ID that ends in an "_x" can cross hybridize. Once you have this you can double check results like that shown above to see if the probe in question is known to cross hybridize to the listed Entrez genes.