How do I convert Affymetrix ID names to gene names

Question

[dannoh]

How do I convert the row names of the intensity value ("1007_s_at" "1053_at" "117_at" "121_at" "1255_g_at") from the HG-U133_Plus_2 Affymetrix Human Genome U133 Plus 2.0 Array to gene names from the official CDF? This there a online tutorial somewhere? Thanks

[Michael]

See: Converting Affymetrix Probes To Gene Ids

[orzech_mag]

You can use some web tools, e.g. DAVID Resources Converter.

[Manvendra Singh]

biomart is useful for you

Answer 1

[Kevin Blighe]

Answers here:

• A: Affymetrix Human Genome U133 Plus 2.0 Array
• A: Annotate Affymetrix probesets to Gene symbols

Kevin

[afli]

Hi, kevin. If I have the probe fasta file(http://www.affymetrix.com/Auth/analysis/downloads/data/Rice.probe_fasta.zip), how can I know which probe correspond to which gene? Because each gene correspond to one probe sets, which contain ~24 probes, this makes blast job a bit hard. BTW, I have the correspondence list of one version(version A), using one reference genome. But my genome is some different from this reference genome, just using version A may lose some genes, I want to know if I can make the correspondence of gene name and probe id with my own genome? Is there any tool to do this? Thank you!

Aifu.

[Kevin Blighe]

Wait, it should be:

• probe: 25nt sequence that targets a particular part of an exon
• probe-set: multiple probes that 'tile' across an exon, targeting different parts

Multiple probe-sets, then, form a gene. Note that a probe-set may consist of just a single probe.

I'm not sure what you are aiming to do? - determine that target gene for your probe sequences?

[afli]

I want to determine the target gene for the probe sequences, with the microarray data in hand, I can do differential expression analysis to find meaningful genes.

[Kevin Blighe]

You should download the annotation files from Affymetrix and then link these to the probe IDs (I think). I have never analysed rice.

[afli]

yes, I download one and know the correspondence, but the affymetrix was based on one variety A. Now it is used on another variety B, the correspondence in A variety maynot as same as B, though there are many homologs, B may have new genes such as duplicated genes. Affymetrix may show the signal of these new genes. So I want to know how to produce that correspondence file for B by myself.

[Kevin Blighe]

I see, you are studying variety B, for which Affymetrix has no microarray?

[afli]

Sorry for this confusion, I am studying variety B, it do have microarray, but the Affymetrix was design on variety A.

[Kevin Blighe]

You are limited, therefore, to the probes that are included on the microarray. If you wanted to identify novel transcripts in B, you could do RNA-seq.

[afli]

Thank you for your suggestion, kevin.