HI,

I have a quick question regarding the annotation package for HuGene2.0 array. Previously with the pd.hugene.2.0.st_3.10.0 package (R_3.1.3, oligo_1.30.0), I was able to find annotation related to the gene PTEN, however, when I updated the package to pd.hugene.2.0.st_3.14.1 (R_3.2.1, oligo_1.32.0), I got NA for geneassignment  (attached below):

> features <- pData(featureData(dataset$eset))
> features <- features[features$category == 'main',c('transcriptclusterid','seqname','start','stop','geneassignment','mrnaassignment', 'unigene')];
>  x <- features[features$transcriptclusterid == '16707030',]
> str(x)
'data.frame':    1 obs. of  7 variables:
 $ transcriptclusterid: int 16707030
 $ seqname            : chr "chr10"
 $ start              : int 89622870
 $ stop               : int 89731687
 $ geneassignment     : chr "ENST00000371953 // PTEN // phosphatase and tensin homolog // 10q23.3 // 5728 /// NM_000314 // PTEN // phosphatase and tensin ho"| __truncated__
 $ mrnaassignment     : chr "ENST00000371953 // ENSEMBL // cdna:known chromosome:GRCh37:10:89622870:89731687:1 gene:ENSG00000171862 gene_biotype:protein_cod"| __truncated__
 $ unigene            : chr "ENST00000371953 // Hs.500466 // adipose tissue| adrenal gland| bladder| blood| bone| brain| cervix| connective tissue| ear| emb"| __truncated__

-------------------------------------------------------------------------------------------------------------------------------------

> features <- pData(featureData(dataset$eset));

> features <- features[features$category == 'main',c('transcriptclusterid','seqname','start','stop','geneassignment','mrnaassignment', 'unigene')];

> x <- features[features$transcriptclusterid == '16707030',]
> str(x)
'data.frame':    1 obs. of  7 variables:
 $ transcriptclusterid: int 16707030
 $ seqname            : chr "chr10"
 $ start              : int 89622870
 $ stop               : int 89731687
 $ geneassignment     : chr NA
 $ mrnaassignment     : chr NA
 $ unigene            : chr NA

Thank,

Sylvia

The annotation data that we supply is basically just a re-packaging of the Affymetrix csv annotation files. In the case of the pd.hugene.2.0.st package it is a direct read-in of that file, whereas in the hugene20sttranscriptcluster.db package we take Affy's mapping of probeset ID ->Entrez Gene ID and then do all the further mappings from the Gene ID. But in the end the results are pretty much the same.

Affymetrix does update their annotation csv files, and we use the most updated version thereof. At this point we are using the na35 versions, which no longer say that 16707030 measures PTEN:

grep 16707030 HuGene-2_0-st-v1.na33.2.hg19.transcript.csv | cut -d, -f 2,3,5,6,8
"16707030","chr10","89622870","89731687","ENST00000371953 // PTEN // phosphatase and tensin homolog // 10q23.3 // 5728 /// NM_000314 // PTEN // phosphatase and tensin homolog // 10q23.3 // 5728"
grep 16707030 HuGene-2_0-st-v1.na35.hg19.transcript.csv | cut -d, -f 2,3,5,6,8
"16707030","chr10","89622870","89731687","---"

Anyway, if you were to go to netaffx, get the sequence that they say that transcript interrogates, and blat that at UCSC, it doesn't look like it overlaps PTEN (the sequence is the black bar labeled 'Your Sequence from Blat Search').