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Question: Annotation for Mouse Illumina Expression Chip V6.1.1
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gravatar for smt8n
16 months ago by
smt8n0
smt8n0 wrote:

Dear all,

 

I am trying to look at a relatively old mouse data that was taken using Expression Chip v6.1.1. The problem came I when I tried to convert Probe IDs to gene names. Probe IDs are, for example: 10243, 10280, 10575, 20048, ..., 102900072, 102900075, ...

 

I tried an old keys/mapIds way using 3 packages: illuminaMousev1.db, illuminaMousev1.1.db, illuminaMousev2.db and none had Probe IDs similar to what I got from GEO file

 

As an example of how I did it:

toget <- c("GENENAME","SYMBOL","ENTREZID","ENSEMBL", "ACCNUM")

library("illuminaMousev1.db")

ks <- keys(illuminaMousev1.db)

annData1 <- as.data.frame(lapply(toget, function(x) mapIds(illuminaMousev1.db, ks, x, "PROBEID")))

 

I eventually (possibly) succeeded using 

genes <- probeID2nuID(probes, lib.mapping = "lumiMouseIDMapping"[,"Symbol"]

 

from lumi (I was using lumi for reading/normalizing anyway), but when I started investigating duplicate gene entries and presumably transcript variants, I felt a need to double check the conversion. Does anybody have a suggestion?

 

By the way, when I try

getSYMBOL(380091,"lumiMouseIDMapping")

(380091 being a probe ID for one of genes with name repeated multiple times and with different, according to google, transcript variants) I get

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘columns’ for signature ‘"function"’

 

Thank you 

ADD COMMENTlink modified 16 months ago by Andy Lynch80 • written 16 months ago by smt8n0
0
gravatar for Andy Lynch
16 months ago by
Andy Lynch80
United Kingdom
Andy Lynch80 wrote:

Hi Smt8n,

Those look to me to be ArrayAddressIDs that are in illuminaMousev1p1.db. An (inelegant) approach to extracting them would be:

library("illuminaMousev1p1.db")

library(DBI)

fullanno<-illuminaMousev1p1fullReannotation()
fullanno[fullanno$ArrayAddress %in% c(10243, 10280, 10575, 20048, 102900072, 102900075),c(2,12,13,16)]
      ArrayAddress           GenomicLocation SymbolReannotated EnsemblReannotated
3222     102900075  chr6:31372368:31372417:+          AK052154               <NA>
3934     102900072 chr11:62141678:62141727:+             Ncor1 ENSMUSG00000042298
9122         10280 chr11:99712245:99712294:-         Krtap4-16 ENSMUSG00000046474
16521        20048  chr7:31455862:31455911:-     4930479M11Rik ENSMUSG00000049761
19514        10575 chr13:73819014:73819063:-           Slc6a19 ENSMUSG00000021565
20442        10243  chr5:34839459:34839508:-             Tnip2 ENSMUSG00000059866

 

I hope that helps.

Andy

 

ADD COMMENTlink written 16 months ago by Andy Lynch80
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