Question: Affymetrix probeset IDs...
0
gravatar for a11msp
6.6 years ago by
a11msp110
European Union
a11msp110 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
ADD COMMENTlink modified 4.6 years ago by srinivasnvnk550 • written 6.6 years ago by a11msp110
5
gravatar for komal.rathi
6.6 years ago by
komal.rathi3.7k
Children's Hospital of Philadelphia, Philadelphia, PA
komal.rathi3.7k 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 COMMENTlink modified 6.6 years ago • written 6.6 years ago by komal.rathi3.7k

Thanks a lot, will try this out tomorrow!

ADD REPLYlink written 6.6 years ago by a11msp110

Perfect, it worked, thanks so much!

ADD REPLYlink written 6.6 years ago by a11msp110

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

ADD REPLYlink written 3.7 years ago by waiwaihuhuyiyi0
0
gravatar for benhrif.oussama
5.7 years ago by
benhrif.oussama0 wrote:

Hello ,

what is the solution if i have a human data ?

Thanks

ADD COMMENTlink written 5.7 years ago by benhrif.oussama0

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 REPLYlink written 4.6 years ago by komal.rathi3.7k
0
gravatar for srinivasnvnk55
4.6 years ago by
srinivasnvnk550 wrote:

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

ADD COMMENTlink written 4.6 years ago by srinivasnvnk550
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