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Question: Annotation using IlluminaHumanv3.db
1
17 months ago by
christina.fjeldbo10 wrote:

I am trying to annotate my Illumina data with more updated annotations than the manifest file from Illumina. I have thus tried the IlluminaHumanv3.db, but I get a lot of inconsistent results and are confused about what annotations to use.  For example: The probe ILMN_1736007 have no annotation using the illuminaHumanv3SYMBOL or illuminaHumanv3ENTREZID. However, using the reannotation it is annotated to A1BG with Entrez-ID 1, which is the same annotation as in the Illumina manifest file. Why is it not annotated using the illuminaHumanv3ENTREZID?

mget("ILMN_1736007",illuminaHumanv3PROBESEQUENCE)
#$ILMN_1736007 #[1] "GCAGAGCTGGACGCTGTGGAAATGGCTGGATTCCTCTGTGTTCTTTCCCA" mget("ILMN_1736007",illuminaHumanv3SYMBOL) #$ILMN_1736007
#[1] NA
mget("ILMN_1736007",illuminaHumanv3ENTREZID)
#$ILMN_1736007 #[1] NA mget("ILMN_1736007",illuminaHumanv3SYMBOLREANNOTATED) #$ILMN_1736007
#[1] "A1BG"
mget("ILMN_1736007",illuminaHumanv3ENTREZREANNOTATED)
#$ILMN_1736007 #[1] "1" mget("ILMN_1736007",illuminaHumanv3PROBEQUALITY) #$ILMN_1736007
#[1] "Perfect***"

Another issue is that the Entrez-ID is lost in the reannotation, but the symbol is retained. For example:

mget("ILMN_1814353",illuminaHumanv3SYMBOL)
#$ILMN_1814353 #[1] "ARGFXP2" mget("ILMN_1814353",illuminaHumanv3ENTREZID) #$ILMN_1814353
#[1] "503640"
mget("ILMN_1814353",illuminaHumanv3SYMBOLREANNOTATED)
#$ILMN_1814353 #[1] "ARGFXP2" mget("ILMN_1814353",illuminaHumanv3ENTREZREANNOTATED) #$ILMN_1814353
#[1] NA
mget("ILMN_1814353",illuminaHumanv3PROBEQUALITY)
#\$ILMN_1814353
#[1] "Perfect"

Also, what is the difference between a Perfect and a Perfect**** probe?