So many unmapped probes
2
0
Entering edit mode
Ed Siefker ▴ 230
@ed-siefker-5136
Last seen 6 weeks ago
United States

I have microarray data downloaded from ArrayExpress.  The annotation is listed as "pd.hugene.1.0.st.v1".  I'm trying to annotate them with hugene10sttranscriptcluster.db.  My problem is that a large number of probes map to no symbol or refseq.  Is this normal?

```

> mydata.rma
ExpressionSet (storageMode: lockedEnvironment)
assayData: 33297 features, 14 samples
  element names: exprs
protocolData
  rowNames: GSM946485_48-2.CEL GSM946484_48-1.CEL ... GSM946472_0-1.CEL
    (14 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: GSM946485_48-2.CEL GSM946484_48-1.CEL ... GSM946472_0-1.CEL
    (14 total)
  varLabels: Source.Name Comment..Sample_source_name. ...
    FactorValue..TIME. (27 total)
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.hugene.1.0.st.v1
> ids<-rownames(exprs(mydata.rma))
> length(ids)
[1] 33297
> symbols <- AnnotationDbi::mapIds(hugene10sttranscriptcluster.db, ids, "SYMBOL", "PROBEID")
'select()' returned 1:many mapping between keys and columns
> sumis.na(symbols))
[1] 11147
>
```
A third of these probes match no symbol.  That seems really high.  What's going on?  Is this the wrong .db package to use for this platform?

annotation hugene10sttranscriptcluster.db annotation • 584 views
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2
Entering edit mode
@james-w-macdonald-5106
Last seen 7 hours ago
United States

Your counting is off, primarily because you are naively assuming that everything on an Affy array actually measures something that should have a gene symbol.

con <- db(pd.hugene.1.0.st.v1)

> ids <- dbGetQuery(con, "select transcript_cluster_id from featureSet where type='1';")[,1]
> length(ids)
[1] 253002

> sum(is.na(mapIds(hugene10sttranscriptcluster.db, as.character(ids), "ENTREZID","PROBEID")))
'select()' returned 1:many mapping between keys and columns
[1] 7567

Which means that about 4.4% of the 'main' probes have no Entrez Gene ID, and are probably some speculative content, or lincRNAs or whatnot.

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0
Entering edit mode
@jennietodd141-15189
Last seen 4.9 years ago

Great post, I have seen excellent expression in your writing

mangahere

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