Question

Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?

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naf • 0

@naf-20627

Last seen 5.6 years ago

Hello, I am having a problem with the annotation of probes for the Affymetrix and the Illumina platforms data,

I am using the package (hgu133plus2.db BiocManager:version 3.8 for R 3.5.2 version) for the Affymetrix data and "org.Hs.eg.db" for the Illumina data.

When I use the command (Affymetrix):

annotation <- select(hgu133plus2.db,keytype='PROBEID', keys=PROBEID, columns = c("ENTREZID"))

or (for Illumina):

annotation <- select(org.Hs.eg.db,keytype = 'ENTREZID',keys = ENTREZID,columns = c('SYMBOL'))

I get the following similar error messages in both cases:

For Affymetrix:

Error in select(hgu133plus2.db, keytype = "PROBEID", keys = PROBEID, columns = c("ENTREZID")) : unused arguments (keytype = "PROBEID", keys = PROBEID, columns = c("ENTREZID"))

For Illumina:

Error in select(org.Hs.eg.db, keytype = "ENTREZID", keys = ENTREZID, columns = c("SYMBOL")) : unused arguments (keytype = "ENTREZID", keys = ENTREZID, columns = c("SYMBOL"))

Has anyone also encountered this type of error, is it just a "silly" mistake or does it have to do with some more complicated reason?

Affymetrix Illumina probes microarray annotation package • 2.4k views

ADD COMMENT • link updated 5.6 years ago by Guido Hooiveld ★ 4.1k • written 5.6 years ago by naf • 0

score 0 · Answer 1 · 2019-05-07

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Guido Hooiveld ★ 4.1k

@guido-hooiveld-2020

Last seen 14 minutes ago

Wageningen University, Wageningen, the …

You didn't post your complete code, but have you assigned some IDs (probeset IDs resp. EntrezGene IDs) to the (your) 'variables' PROBEID resp. ENTREZID? I am asking because you code as such should work....(see below). Two remarks: I wouldn't recommend naming your variable that contains the probe/entrez IDs the same as one of the possible keytype arguments. Also have a look at the (1st) vignette of the package AnnotationDbi here.

> # load the annotation library
> library(org.Hs.eg.db)
> 
> # as sample data, select the first 15 entrez/gene IDs.
> ENTREZID <- keys(org.Hs.eg.db)[1:15]
> 
> # retrieve relevant annotation info
> select(org.Hs.eg.db, keytype = "ENTREZID", keys = ENTREZID, columns = c("SYMBOL") )
'select()' returned 1:1 mapping between keys and columns
   ENTREZID   SYMBOL
1         1     A1BG
2         2      A2M
3         3    A2MP1
4         9     NAT1
5        10     NAT2
6        11     NATP
7        12 SERPINA3
8        13    AADAC
9        14     AAMP
10       15    AANAT
11       16     AARS
12       17    AAVS1
13       18     ABAT
14       19    ABCA1
15       20    ABCA2
> 
>

ADD COMMENT • link 5.6 years ago Guido Hooiveld ★ 4.1k

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Thank you for your prompt answer Guido.

Unfortunately still getting the error message. I have assigned some IDs (probeset IDs resp. EntrezGene IDs) to my variables' PROBEID resp. ENTREZID. I have even tried to copy-paste your code but keep on getting the same discouraging message. This is where I assign values to ENTREZID in my code:

ENTREZID <- rownames(dge$counts)

keytypes(org.Hs.eg.db)

columns(org.Hs.eg.db)

annotation <- select(org.Hs.eg.db,keytype = 'ENTREZID',keys = ENTREZID,columns = c('SYMBOL'))

I get:

`[1] "ACCNUM" "ALIAS" "ENSEMBL" "ENSEMBLPROT" "ENSEMBLTRANS" [6] "ENTREZID" "ENZYME" "EVIDENCE" "EVIDENCEALL" "GENENAME"
[11] "GO" "GOALL" "IPI" "MAP" "OMIM"
[16] "ONTOLOGY" "ONTOLOGYALL" "PATH" "PFAM" "PMID"
[21] "PROSITE" "REFSEQ" "SYMBOL" "UCSCKG" "UNIGENE"
[26] "UNIPROT"
[1] "ACCNUM" "ALIAS" "ENSEMBL" "ENSEMBLPROT" "ENSEMBLTRANS" [6] "ENTREZID" "ENZYME" "EVIDENCE" "EVIDENCEALL" "GENENAME"
[11] "GO" "GOALL" "IPI" "MAP" "OMIM"
[16] "ONTOLOGY" "ONTOLOGYALL" "PATH" "PFAM" "PMID"
[21] "PROSITE" "REFSEQ" "SYMBOL" "UCSCKG" "UNIGENE"
[26] "UNIPROT"

This is the error I get again:

Error in select(org.Hs.eg.db, keytype = "ENTREZID", keys = ENTREZID, columns = c("SYMBOL")) :

unused arguments (keytype = "ENTREZID", keys = ENTREZID, columns = c("SYMBOL"))``

ADD REPLY • link 5.6 years ago naf • 0

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You probably have select masked by another package. Try

AnnotationDbi::select(org.Hs.eg.db, ENTREZID, "SYMBOL", "ENTREZID")

ADD REPLY • link 5.6 years ago James W. MacDonald 67k

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absolutely magic James, thanks so much, it's working!!

ADD REPLY • link 5.6 years ago naf • 0

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Hi James,

I now have another problem with annotations with these files:

the illumina textfiles found in:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5350, the datafile GSE5350MAQCILM12359TXTs.zip

When I used:

AnnotationDbi::select(org.Hs.eg.db,keytype = 'ENTREZID',keys = ENTREZID,columns = c('SYMBOL'))

I got the error message:

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

I went on the internet and saw that what I have in my files are not entrezID's, I have probe iD's that look like:

"GI13376332-S" "GI13376334-S" "GI13376338-S" "GI13376342-S"

I saw that some years back, some other people had a similar problem and you helped them solve it. I read about FLYBASE ID's and PROBE ID's but I just can't find what type of ID's mine are. Do you have an idea?

I tried this:

AnnotationDbi::select(org.Hs.eg.db,rownames(dge$counts),"SYMBOL","TargetID")

I know that "TargetID" is not right but I just don't know what type of ID Illumina has used.

ADD REPLY • link 5.6 years ago naf • 0

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The illuminaHumanv1.db package has mappings between this Illumina chip and Symbol, entrez, etc. The keytype you need to use is PROBEID

library(illuminaHumanv1.db)
anno <- select(illuminaHumanv1.db, keytype="PROBEID",keys=ENTREZID,columns=c("ENTREZID","SYMBOL"))
head(anno)

ADD REPLY • link 5.6 years ago Mark Dunning ★ 1.1k

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great Mark, thanks a lot,

it worked but with adding "AnnotationDbi::" just in front of select.... as James W. MacDonald (above) suggested,

thanks a stack!

ADD REPLY • link 5.6 years ago naf • 0