Question: Transform Affymetrix Ids Between Species
0
gravatar for mimA
8.2 years ago by
mimA30
European Union
mimA30 wrote:

Hi all,

Is there a way to transform chick Affymetrix identifiers into human/mouse accession numbers?I've heard that R is quite useful in this regard but does anyone know which function/package can be used or if there are other online available tools? My chick Affymetrix Ids look like this:

AFFX-Gga-actin-M_at
AFFX-Gga-ef1a-3_s_at
AFFX-Gga-ef1a-5_s_at
AFFX-Gga-ef1a-M_s_at
AFFX-Gga-gapdh-3_a_at
AFFX-Gga-gapdh-3_a_at
AFFX-Gga-gapdh-3_x_at
AFFX-Gga-gapdh-3_x_at
AFFX-Gga-gapdh-5_a_at
AFFX-Gga-gapdh-5_a_at
AFFX-Gga-gapdh-M_a_at
AFFX-Gga-gapdh-M_a_at
AFFX-Gga-gapdh-M_a_at
Gga.1.1.S1_at
Gga.100.1.S1_a_at
Gga.1000.1.S1_at
Gga.10000.1.S1_s_at
Gga.10003.1.S1_at

Thanks.

R • 1.2k views
ADD COMMENTlink modified 6.0 years ago by Biostar ♦♦ 20 • written 8.2 years ago by mimA30
3
gravatar for Steve Lianoglou
8.2 years ago by
Steve Lianoglou5.1k
US
Steve Lianoglou5.1k wrote:

One way is to use the annotationTools package, its vignette outlines the exact use case you are asking about.

You can always use biomaRt, too, but maybe you can start with that.

ADD COMMENTlink written 8.2 years ago by Steve Lianoglou5.1k
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