Hello Mark,

I'm writing to report an apparent error in the illuminaHumanv4.db package,
version 1.20.0.  Specifically, the mapping for "C16ORF15" in ALIAS2PROBE
appears to be incorrect.  Below is an R code snippet:

library("illuminaHumanv4.db")
packageVersion("illuminaHumanv4.db")
# [1] '1.20.0'
#
http://www.bioconductor.org/packages/release/data/annotation/html/illuminaHumanv4.db.html

# Define some mappings
xxAP <- as.list(illuminaHumanv4ALIAS2PROBE)
xxS <- as.list(illuminaHumanv4SYMBOL)

# Compare these two:
xxS[xxAP[["C16ORF15"]]]
xxS[xxAP[["C16orf15"]]]

# I get:
# > xxS[xxAP[["C16ORF15"]]]
# $ILMN_1718060
# [1] "OTUD7A"
# $ILMN_1785146
# [1] "OTUD7A"
# $ILMN_2298160
# [1] "OTUD7A"
#
# > xxS[xxAP[["C16orf15"]]]
# $ILMN_1693042
# [1] "WDR90"
# $ILMN_1698185
# [1] "WDR90"

According to HGNC (via DuckDuckGo):
OTUD7A (OTU domain containing 7A)
Protein-coding gene on human chromosome 15q13.1, also known as *C15orf16*,
CEZANNE2, OTU domain containing 7, OTUD7, chromosome 15 open reading frame
16.

WDR90 (WD repeat domain 90)
Protein-coding gene on human chromosome 16p13.3, also known as *C16orf15*,
C16orf16, C16orf17, C16orf18, C16orf19, FLJ36483, KIAA1924, chromosome 16
open reading frame 15, chromosome 16 open reading frame 16, chromosome 16
open reading frame 17, chromosome 16 open reading frame 18, chromosome 16
open reading frame 19.

So it appears the ALIAS2PROBE mapping for C16ORF15 is actually for
C15orf16.  Indeed,
all.equal(xxAP[["C16ORF15"]], xxAP[["C15orf16"]])
# [1] TRUE

Some questions:
1) Why is there a mapping for both C16orf15 and C16ORF15?
2) Can you make the names for mappings like ALIAS2PROBE all upper case?
Perhaps there is a Bioconductor annotation convention that prevents this?
3) I also noticed:
nms <- names(xxAP)
length(nms); length(unique(nms)); length(unique(toupper(nms)))
# [1] 99696
# [1] 99696
# [1] 99378
Is there potentially a problem with the 300-odd names that are no longer
unique when raised to upper case?

Regards,

_Taku

 Taku A. Tokuyasu, PhD
Computational Biology Core
UCSF Helen Diller Family Comprehensive Cancer Center

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