Question: Map exon level probeset to gene level probeset - Huex ST1.0
0
gravatar for GENOMIC_region
7 months ago by
GENOMIC_region0 wrote:

Hi all,  

I've HuEx ST1.0 microarray data. Using Oligo package I get gene level expression (RMA, target=core) and for exon probes I get expression using RMA (target = probeset).   

I'd like to map the probesets from exon level expression to genes. 

I've HuEx-1_0-st-v2.na36.hg19.transcript.csv and HuEx-1_0-st-v2.na30.hg19.probeset.csv data with me.

How do I proceed? 

 

 

 

ADD COMMENTlink modified 7 months ago by James W. MacDonald50k • written 7 months ago by GENOMIC_region0
Answer: Map exon level probeset to gene level probeset - Huex ST1.0
2
gravatar for James W. MacDonald
7 months ago by
United States
James W. MacDonald50k wrote:
> library(oligo)

> library(pd.huex.1.0.st.v2)

> con <- db(pd.huex.1.0.st.v2)
> zz <- dbGetQuery(con, "SELECT fid, fsetid, core_mps.transcript_cluster_id as meta_fsetid FROM pmfeature INNER JOIN core_mps USING(fsetid)")
> head(zz, 28)
       fid  fsetid meta_fsetid
1   211994 3948549     3948543
2  1471688 3948549     3948543
3  3805884 3948549     3948543
4  4551478 3948549     3948543
5   370423 3948555     3948543
6  4054561 3948555     3948543
7  4525508 3948555     3948543
8  4868017 3948555     3948543
9  3803159 3948556     3948543
10 4038604 3948556     3948543
11 5052410 3948556     3948543
12 6529617 3948556     3948543
13 3773083 3948570     3948543
14 4098009 3948570     3948543
15 4284637 3948570     3948543
16 4615290 3948570     3948543
17 1287610 3948572     3948543
18 2815899 3948572     3948543
19 5185828 3948572     3948543
20 5267844 3948572     3948543
21  183062 3948577     3948543
22 1491481 3948577     3948543
23 2179919 3948577     3948543
24 4491964 3948577     3948543
25   17105 3948584     3948543
26 2838641 3948584     3948543
27 4661580 3948584     3948543
28 5698119 3948584     3948543

Here the fid is the individual probe, fsetid is the PSR (probe set region), which isn't really an exon. It may well be just part of an exon. But that is the ID for what you are calling the exon level expression. The meta_fsetid contains the IDs for what you are calling 'gene level expression'. And you can see here how 28 probes are collected into seven PSRs, which are then collected into one meta_fsetid.

ADD COMMENTlink written 7 months ago by James W. MacDonald50k

Thank you very much. :)

ADD REPLYlink written 7 months ago by GENOMIC_region0
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