Affy Mouse Annotation
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Entering edit mode
trhood • 0
@trhood-15406
Last seen 3.5 years ago

Hello!

I have a question about associating probeIDs from an Affy GeoDataset GSE85507, I downloaded the series matrix and got the normalized data file with 17000+ probes and 283 samples. I tried to associate the ID_REF numbers (example "6747308") using the moex10stprobeset.db, the dataset says they used "[MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [transcript (gene) version]". I keep getting an error message that says the probe ids are not valid for that database. Are these numbers not actually probe ids? How do I know how to associate them to the mgi_symbol? 

 

My code: 

library(dplyr)
library(AnnotationDbi)
library(moex10stprobeset.db)

#set working directory
setwd(".../GeoDownloads/GSE85507")

#load the data

e <- read.csv("data.csv", stringsAsFactors = FALSE)
clin <- read.csv("clin.csv", stringsAsFactors = FALSE)

#get probeIDs
ids <- e$ID_REF

# map the ids
mapped_ids <- mapIds(moex10stprobeset.db, keys=as.character(ids), c("SYMBOL"), keytype="PROBEID")

 

########

Error message:

Error in .testForValidKeys(x, keys, keytype, fks) : 
  None of the keys entered are valid keys for 'PROBEID'. Please use the keys method to see a listing of valid arguments.

annotation affymetrix • 439 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 8 hours ago
United States

As you have already noted, the data you have are the transcript level probesets, so you need the moex10sttranscriptcluster.db package, not the probeset version.

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