Mapping probe id's to gene symbols
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Entering edit mode
3.2 years ago
bio94 ▴ 50

Hello everyone, I was wondering as to how do I map the probe id's to the gene symbols so that they are in the same order. I just noticed that my annotLookup table probe id's are in a different order when compared to the original dataset.

> rownames(exprs(gset))[1:10]
 [1] "1007_s_at" "1053_at"   "117_at"    "121_at"    "1255_g_at" "1294_at"   "1316_at"   "1320_at"   "1405_i_at"
[10] "1431_at"  

> annotLookup <- getBM(mart=mart, attributes=c("affy_hg_u133_plus_2", "external_gene_name"), filter="affy_hg_u133_plus_2", values <- rownames(exprs(gset))[1:10] , uniqueRows=TRUE)

> head(annotLookup)
  affy_hg_u133_plus_2 external_gene_name
1             1294_at            MIR5193
2             1316_at               THRA
3             1294_at               UBA7
4           1007_s_at               DDR1
5             1320_at             PTPN21
6              117_at              HSPA6

Thank you!

mapping probeid genesymbols biomart annotate • 2.0k views
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add two more steps to your analysis. Results data has probes with multiple gene names/symbols. You can collapse them @ bio94

> probes$V1
 [1] "1007_s_at" "1053_at"   "117_at"    "121_at"    "1255_g_at" "1294_at"  
 [7] "1316_at"   "1320_at"   "1405_i_at" "1431_at":
> results1=aggregate(external_gene_name ~., results, toString)
> na.omit(results1[match(probes$V1, results1$affy_hg_u133_plus_2),])
  affy_hg_u133_plus_2 external_gene_name
1           1007_s_at               DDR1
2              117_at              HSPA6
3             1294_at      MIR5193, UBA7
4             1316_at               THRA
5             1320_at             PTPN21
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Thanks very much Emily

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3
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3.2 years ago

You can't. BioMart orders things by the order in its database, not by how you've ordered them.

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I was in the process of taking the user through it:

C: Annotate Affymetrix probesets to Gene symbols

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