corresponding gene names for probeIDs

Question

[nazaninhoseinkhan]

Dear all,

I am trying to analyze gene expression data for a bacterial species, S.aureus.

When I investigate corresponding affymetrix celfiles, it has about 362000 lines(probeIDs).

I want to replace probeIDs with gene names.

I got corresponding annotation file, but it has only about 7000 gene names.

Can any body guide me what can I do?

Best

Nazanin

[Keith Callenberg]

Can you post which affy chip you are using? Most microarrays map multiple probes to each gene. I am pretty sure S. aureus does not have more than 7000 genes.

[nazaninhoseinkhan]

Take for example GSM135454.CEL.

How can I realize which probeIDs correspond to a specific gene?

Answer 1

[Manvendra Singh]

How many total genes does this species has?

if total 7000 then do not worry, so there would be many probes targeting one gene, just take mean all probes and assign to its respective gene

[nazaninhoseinkhan]

How can I realize which probeIDs correspond to a specific gene?

In order to take mean I have to know that.

[Manvendra Singh]

Its Affymetrix S. aureus Genome Array it has around 7775 rows representing probe IDs, in your probe_ID list you must have many duplicated ones

Check with

dim(data[!duplicated(data[,probe_ID_coloumn])],)

Answer 2

[kongcin419]

Hi Nazanin,

Have you already successfully map all your probeID to the corresponding gene name? I am also currently working on a set of microarray data for S. aureus. The microarray was performed using the S. aureus GeneChip Genome Array. I normalized my CEL file data using Expression Console and annotated the probe using TAC (S. aureus annotation file from Affymetrix containing 700 odds gene). However, I found that about 50% of the probe ID did not have a corresponding gene symbol/gene name.

If you have done yours, could you please share how to map all the probe ID to a gene name?

Thank you.