Question: How do I convert Affymetrix ID names to gene names
1
gravatar for dannoh
5.0 years ago by
dannoh10
United States
dannoh10 wrote:

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

R • 18k views
ADD COMMENTlink modified 18 months ago by Kevin Blighe54k • written 5.0 years ago by dannoh10
1

See: Converting Affymetrix Probes To Gene Ids

ADD REPLYlink written 5.0 years ago by Michael Dondrup47k

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

ADD REPLYlink written 5.0 years ago by orzech_mag210

biomart is useful for you

ADD REPLYlink written 5.0 years ago by Manvendra Singh2.1k
1
gravatar for Kevin Blighe
18 months ago by
Kevin Blighe54k
Kevin Blighe54k wrote:

Answers here:

Kevin

ADD COMMENTlink written 18 months ago by Kevin Blighe54k

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.

ADD REPLYlink modified 16 months ago • written 16 months ago by afli190

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?

ADD REPLYlink written 16 months ago by Kevin Blighe54k

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.

ADD REPLYlink written 16 months ago by afli190

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

ADD REPLYlink written 16 months ago by Kevin Blighe54k

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.

ADD REPLYlink modified 16 months ago • written 16 months ago by afli190

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

ADD REPLYlink written 16 months ago by Kevin Blighe54k

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

ADD REPLYlink written 16 months ago by afli190
1

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.

ADD REPLYlink written 16 months ago by Kevin Blighe54k

Thank you for your suggestion, kevin.

ADD REPLYlink written 16 months ago by afli190
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