Microarray: Build annotation for HT MG430PM affymetrix
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@c3222841
Last seen 4 months ago
France

Hello I'm new to affymetrix analysis and have been following several tutorial to analyze microarrays.

I have to analyze a specific microarray (GSE33948 - GPL11180) that used the HT MG430PM array plate, but I can't find any annotation package for this specific plate.

I have found some files that could help me building the annotation http://www.affymetrix.com/support/technical/byproduct.affx?product=ht_mg-430_pm_ap but i don't know how to do it on my own.

Thank you, PA

AffymetrixChip Microarray affymetrix • 184 views
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Guido Hooiveld ★ 3.0k
@guido-hooiveld-2020
Last seen 2 days ago
Wageningen University, Wageningen, the …

Hi, It is actually quite straightforward to do using the library AnnotationForge. Using the (extracted) file form the link you provided: "HT_MG-430_PM.na36.annot.csv".

> # set working directory to location of the csv file
> setwd("E:\\working\\dir")
> 
> # install/update required (annotation) libraries.
> # The ChipDb that will be generated will link to the
> # content of the OrgDb "org.Mm.eg.db", so better be
> # up-to-date. Idem for GO.db.
> 
> BiocManager::install("AnnotationForge")
> BiocManager::install(c("mouse.db0", "org.Mm.eg.db", "GO.db"))
>
> # load required library
> library("AnnotationForge")
>
> # generate ChipDb (in working directory)
> # note: you can ignore the warnings!
> makeDBPackage("MOUSECHIP_DB",
+    affy = TRUE,
+    prefix="htmg430pm",
+    fileName="HT_MG-430_PM.na36.annot.csv",
+    baseMapType="gbNRef",
+    outputDir=".",
+    version = "3.12.0", #current BioC version
+    manufacturer="Affymetrix",
+    chipName = "htmg430pm",
+    manufacturerUrl="http://www.affymetrix.com")
baseMapType is gb or gbNRef
Prepending Metadata
Creating Genes table
Appending Probes
Found 45124 Probe Accessions
Appending Gene Info
Found 37609 Gene Names
Found 37609 Gene Symbols
Appending Chromosomes
Appending RefSeq
Appending Pubmed
Appending Unigene
Appending ChrLengths
Appending 3 GO tables
Appending 3 GO ALL tables
Appending KEGG
Appending EC
Appending Chromosome Locations
Appending Pfam
Appending Prosite
Appending Alias
Appending Ensembl
Appending Uniprot
Appending MGI
Appending Metadata 


simplifying probes table
dropping redundant data
Creating package in ./htmg430pm.db 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> 
> # Done, but also need to install in R!
> install.packages("./htmg430pm.db", repos=NULL, type = "source")
* installing *source* package 'htmg430pm.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'htmg430pm.db'
    finding HTML links ... done
    htmg430pmACCNUM                         html  
    htmg430pmALIAS2PROBE                    html  
    htmg430pmBASE                           html  
    htmg430pmCHR                            html  
    htmg430pmCHRLENGTHS                     html  
    htmg430pmCHRLOC                         html  
    htmg430pmENSEMBL                        html  
    htmg430pmENTREZID                       html  
    htmg430pmENZYME                         html  
    htmg430pmGENENAME                       html  
    htmg430pmGO                             html  
    htmg430pmMAPCOUNTS                      html  
    htmg430pmMGI                            html  
    htmg430pmORGANISM                       html  
    htmg430pmPATH                           html  
    htmg430pmPFAM                           html  
    htmg430pmPMID                           html  
    htmg430pmPROSITE                        html  
    htmg430pmREFSEQ                         html  
    htmg430pmSYMBOL                         html  
    htmg430pmUNIGENE                        html  
    htmg430pmUNIPROT                        html  
    htmg430pm_dbconn                        html  
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (htmg430pm.db)
> 
> # check
> library(htmg430pm.db)
Loading required package: org.Mm.eg.db
> 
> # which keytypes can be queried in database?
> # note: default is 'probeid'
> keytypes(htmg430pm.db)
 [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS"
 [6] "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL"  "GENENAME"    
[11] "GO"           "GOALL"        "IPI"          "MGI"          "ONTOLOGY"    
[16] "ONTOLOGYALL"  "PATH"         "PFAM"         "PMID"         "PROBEID"     
[21] "PROSITE"      "REFSEQ"       "SYMBOL"       "UNIGENE"      "UNIPROT"     
>
> # which annotation info can be retrieved?
> columns(htmg430pm.db)
 [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS"
 [6] "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL"  "GENENAME"    
[11] "GO"           "GOALL"        "IPI"          "MGI"          "ONTOLOGY"    
[16] "ONTOLOGYALL"  "PATH"         "PFAM"         "PMID"         "PROBEID"     
[21] "PROSITE"      "REFSEQ"       "SYMBOL"       "UNIGENE"      "UNIPROT"     
>
> # Let's use it! Obtain annotation info!
> k <- keys(htmg430pm.db)
> 
> res <- AnnotationDbi::select(htmg430pm.db,
+   keys=k[1:10], #limit to first 10 probesets
+   keytype="PROBEID",
+   columns=c("ENTREZID", "SYMBOL", "GO")
+   )
'select()' returned 1:many mapping between keys and columns
> res
            PROBEID ENTREZID   SYMBOL         GO EVIDENCE ONTOLOGY
1     1415670_PM_at    54161    Copg1 GO:0000139      IBA       CC
2     1415670_PM_at    54161    Copg1 GO:0000139      IDA       CC
3     1415670_PM_at    54161    Copg1 GO:0000139      ISO       CC
4     1415670_PM_at    54161    Copg1 GO:0005198      IEA       MF
5     1415670_PM_at    54161    Copg1 GO:0005737      IEA       CC
6     1415670_PM_at    54161    Copg1 GO:0005783      IBA       CC
7     1415670_PM_at    54161    Copg1 GO:0005793      IBA       CC
8     1415670_PM_at    54161    Copg1 GO:0005794      IBA       CC
9     1415670_PM_at    54161    Copg1 GO:0005794      ISO       CC
10    1415670_PM_at    54161    Copg1 GO:0006886      IEA       BP
11    1415670_PM_at    54161    Copg1 GO:0006888      IBA       BP
12    1415670_PM_at    54161    Copg1 GO:0006891      IBA       BP
13    1415670_PM_at    54161    Copg1 GO:0009306      IBA       BP
14    1415670_PM_at    54161    Copg1 GO:0015031      IEA       BP
15    1415670_PM_at    54161    Copg1 GO:0016020      IBA       CC
16    1415670_PM_at    54161    Copg1 GO:0016192      IEA       BP
17    1415670_PM_at    54161    Copg1 GO:0030117      IEA       CC
18    1415670_PM_at    54161    Copg1 GO:0030126      IBA       CC
19    1415670_PM_at    54161    Copg1 GO:0031410      IEA       CC
20    1415670_PM_at    54161    Copg1 GO:0051683      ISO       BP
21    1415670_PM_at    54161    Copg1 GO:0072384      IBA       BP
22    1415670_PM_at    54161    Copg1 GO:0072384      ISO       BP
23    1415671_PM_at    11972 Atp6v0d1 GO:0005515      IPI       MF
24    1415671_PM_at    11972 Atp6v0d1 GO:0005765      IBA       CC
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