Question: Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
0
gravatar for naf
4 months ago by
naf0
naf0 wrote:

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?

ADD COMMENTlink modified 4 months ago by Guido Hooiveld2.5k • written 4 months ago by naf0
Answer: Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
0
gravatar for Guido Hooiveld
4 months ago by
Guido Hooiveld2.5k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.5k wrote:

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 COMMENTlink written 4 months ago by Guido Hooiveld2.5k

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 REPLYlink modified 4 months ago • written 4 months ago by naf0

You probably have select masked by another package. Try

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

ADD REPLYlink written 4 months ago by James W. MacDonald51k

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

ADD REPLYlink written 4 months ago by naf0

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 REPLYlink written 4 months ago by naf0

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 REPLYlink written 4 months ago by Mark Dunning1.1k

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 REPLYlink written 4 months ago by naf0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 288 users visited in the last hour