Affymetrix probeset IDs...

Question: Affymetrix probeset IDs...

6.6 years ago by

a11msp • 110

European Union

a11msp • 110 wrote:

Hi everyone,

I'm trying to look at the processed data for the following ArrayExpress entry:

https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-57818/

The array design for this experiment is specified as " [MoGene-2_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]". (Is it not self-contradictory MoGene-2_0 / Mouse Gene 1.0?).

The problem is that IDs in the processed sample tables look like nothing identifiable not just by me, but also by DAVID's famous ID conversion tool:

ID_REF   VALUE
17364176   6.11692
17306532   4.83607
17450319   6.78837
17260236   4.67415
17513311   7.34779
17217651   6.41337
17380366   10.9677
17548117   9.29091
17225413   6.68588
17458514   10.9731

Does anyone have any idea what these IDs correspond to or there's a problem with these files?

Many thanks!

affymetrix microarray • 6.9k views

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modified 4.6 years ago by srinivasnvnk55 • 0 • written 6.6 years ago by a11msp • 110

6.6 years ago by

komal.rathi • 3.7k

Children's Hospital of Philadelphia, Philadelphia, PA

komal.rathi • 3.7k wrote:

This format is of Affymetrix MoGene-2_0-st annotation data. You can get the corresponding Entrez ID, Gene Symbol & Ensembl ID using:

source("http://bioconductor.org/biocLite.R") biocLite("mogene20sttranscriptcluster.db") library(mogene20sttranscriptcluster.db) Annot <- data.frame(SYMBOL=sapply(contents(mogene20sttranscriptclusterSYMBOL), paste, collapse=","), DESC=sapply(contents(mogene20sttranscriptclusterGENENAME), paste, collapse=","), ENTREZID=sapply(contents(mogene20sttranscriptclusterENTREZID), paste, collapse=","), ENSEMBLID=sapply(contents(mogene20sttranscriptclusterENSEMBL), paste, collapse=","))

Then you can use the Gene Symbol, Entrez ID or Ensembl ID (recommended) to do the DAVID analysis.

ADD COMMENT • link modified 6.6 years ago • written 6.6 years ago by komal.rathi • 3.7k

Thanks a lot, will try this out tomorrow!

ADD REPLY • link written 6.6 years ago by a11msp • 110

Perfect, it worked, thanks so much!

ADD REPLY • link written 6.6 years ago by a11msp • 110

Hi, i'm a R beginner. Can you please show me what should i do after loading those command line?

ADD REPLY • link written 3.7 years ago by waiwaihuhuyiyi • 0

5.7 years ago by

benhrif.oussama • 0

benhrif.oussama • 0 wrote:

Hello ,

what is the solution if i have a human data ?

Thanks

ADD COMMENT • link written 5.7 years ago by benhrif.oussama • 0

Depends on your chip. In the above question, Affymetrix MoGene-2_0-st was used. You can check what is the corresponding annotationdbi package for your chip here.

ADD REPLY • link written 4.6 years ago by komal.rathi • 3.7k

4.6 years ago by

srinivasnvnk55 • 0

srinivasnvnk55 • 0 wrote:

Replace "mogene20sttranscriptcluster" with "hugene20sttranscriptcluster" everywhere including the library

ADD COMMENT • link written 4.6 years ago by srinivasnvnk55 • 0

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