Hello world !


I am working on microarray data (Hugene 2.0 st from affymetrix) and I was willing to get probe-level informations.

For one probeset (fsetid), I need all the different probes (fid) and their chromosome, start, stop, sequence etc.

I know I can get this on NetAffx but as I have to check multiple probesets, I wanted to use the library *oligo* in association with *pd.hugene.2.0.st* 

Here is my code tested on a 'test-list' of 6 .CEL files:

    ## Library loading
    library(oligo)
    library(dplyr)
    library(pd.hugene.2.0.st)
    
    # .CEL importation and read
    celFiles <- list.celfiles('./', full.names=TRUE)
    batch = read.celfiles(celFiles)
    
    # Expression matrix tmp
    tmp=batch@assayData$exprs
    dim(tmp) 
    
    # Connexion pd.hugene.2.0.st@getdb() and normalization
    conn = pd.hugene.2.0.st@getdb()
    norm = rma(batch, background=TRUE,  normalize=TRUE, target="core") 
    
    # Data importation
    tableNames=dbListTables(conn)
    tablesList=list()
    
    for (tableName in tableNames){
      tablesList[[tableName]]=dbGetQuery(conn,paste('SELECT * FROM',tableName))
      print(tableName)
      str(tablesList[[tableName]])
    }
    
    # Simplification of the tablesList dataframe
    testList <- tablesList$featureSet
    testList2 <- tablesList$pmfeature
    testListComplet <- dplyr::full_join(testList, testList2, by = "fsetid")
    
    # Test on one probeset randomly selected : probeset 16730541
    ind = testListComplet$fid[which(testListComplet$fsetid == 16730541)]
    tmp[ind,]
    probeset_test <- subset(testListComplet, fsetid == 16730541)
    probeset_test

Here is the probeset_test result I get :

     fid        fsetid strand     start      stop transcript_cluster_id exon_id crosshyb_type level chrom type     fid   atom   x    y
    153940 16730541      0 102218019 102218094              16730540 5033332             1    NA    11    1  944681 153940  48  586
    153941 16730541      0 102218019 102218094              16730540 5033332             1    NA    11    1 2165196 153941 279 1343

So, according to pd.hugene.2.0.st, for probeset **16730541**, I have 2 probes : **153940 & 153941** with a common start (102218019) and stop (102218094). But when I check on the NetAffx website ( https://www.affymetrix.com/analysis/netaffx/exon/wtgene_probe_set.affx?pk=712:16730541 ), here are the two probes I get :

atcagcggcgccgacaaggagatac	chr11:102218019-102218043 (+)

cagcaaacacggaagctgcgcggct	chr11:102218070-102218094 (+)



Did I do something wrong ? Did I misunderstand something ?
Could you please enlighten me ?!

I am sorry if this is a stupid question but I could not figure it out by myself :(

Thank you so much in advance.


Here is my R info :

    platform       x86_64-apple-darwin15.6.0   
    arch           x86_64                      
    os             darwin15.6.0                
    system         x86_64, darwin15.6.0        
    status                                     
    major          3                           
    minor          4.0                         
    year           2017                        
    month          04                          
    day            21                          
    svn rev        72570                       
    language       R                           
    version.string R version 3.4.0 (2017-04-21)
    nickname       You Stupid Darkness 

 
You are right (almost!).  If you see further in the NetAffx page that you linked

**Probe Set Location:** The genomic location of the probe set for the genome assembly used at array design time (See Genome Source). These coordinates ***begin at the first base of the first probe sequence and end at the last probe of the probe set.***




