The current annotation for Affymetrix HTA 2.0 array is problematic
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tangboyun ▴ 30
@tangboyun-6933
Last seen 5.1 years ago
China

It seems that Affy is silently changing their procedure for the probeset annotation of HTA 2.0.

cut -d"," -f 1,10,13 HTA-2_0.na33.hg19.probeset.csv

"probeset_id","psr_id","probeset_type"
"2824546_st","2824546_st","normgene->exon"
"2824549_st","2824549_st","normgene->exon"
"2824551_st","2824551_st","normgene->exon"
"2824554_st","2824554_st","normgene->exon"
"2827992_st","2827992_st","normgene->exon"
cut -d"," -f 1,10,13 HTA-2_0.na34.hg19.probeset.csv

"probeset_id","psr_id","probeset_type"
"18670005","2824546_st","normgene->exon"
"18670007","2824549_st","normgene->exon"
"18670009","2824551_st","normgene->exon"
"18670011","2824554_st","normgene->exon"
"18670020","2827992_st","normgene->exon"
"18670022","2827995_st","normgene->exon"

cut -d"," -f 1,10,13 HTA-2_0.na35.hg19.probeset.csv

"probeset_id","psr_id","probeset_type"
"18670000","---","Exonic normalization control (Positive Control)"
"18670001","---","Exonic normalization control (Positive Control)"
"18670002","---","Exonic normalization control (Positive Control)"
"18670003","---","Exonic normalization control (Positive Control)"
"18670004","---","Exonic normalization control (Positive Control)"

The probesets in the "main" category are not affected by this changing, as their probeset_name are the same as probeset_id. But all the ctrl probes lost their probeset_type annotations.

> all.probes <- getProbeInfo(dat,field=c('type'), target='probeset')
> unique(all.probes$type)
[1] "main"                       NA 

In na35 probeset annotations, the probeset_type is also changed:

na35, previous
"Positive Control", "pos_control"
"ERCC (External RNA Controls Consortium) step control","control->affx->ercc->step"
"Antigenomic background control", "control->bgp->antigenomic"
"Intronic normalization control (Negative Control)", "normgene->intron"
 "Exonic normalization control (Positive Control)","normgene->exon"

Uers could build na35 annotation db by manually doing the above conversion on "HTA-2_0.na35.hg19.probeset.csv". Currently, Affy hasn't changed the probeset annotation for MTA 1.0 and RTA 1.0 yet ;). 

 

oligo pdInfoBuilder pd.hta.2.0 • 1.6k views
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