100 % Coverage for Gene ID Mapping
I've encounter with some gene ids, not having Entrez ID correspondence and some probe IDs may have same Entrez ID. How do you solve this problem?
biocLite("KEGGdzPathwaysGEO")
#Alzheimer
# Title: Incipient Alzheimer's Disease: Microarray Correlation Analyses
# URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1297
# PMIDs: 14769913
# 9 control 7 disease
data(GSE1297)
data <- GSE1297@assayData$exprs
grp <- as.integer(as.factor(GSE1297@phenoData@data$Group)) - 1
library('hgu133a.db') # here use your chip hgu133a.db
g_ids <- mapIds(hgu133a.db, keys=rownames(data), c("ENTREZID"), keytype="PROBEID")
# Many using same entrez id
> length(which(table(g_ids)>1))
[1] 4805
> sort(table(g_ids),decreasing = T)[1:3]
g_ids
10730 3514 3077
19 17 13
> g_ids[which(g_ids == 10730)]
201351_s_at 201352_at 209671_x_at 210972_x_at 211902_x_at 213830_at 215524_x_at 215540_at
"10730" "10730" "10730" "10730" "10730" "10730" "10730" "10730"
215769_at 215796_at 216133_at 216191_s_at 216304_x_at 216540_at 217056_at 217063_x_at
"10730" "10730" "10730" "10730" "10730" "10730" "10730" "10730"
217065_at 217143_s_at 217397_at
"10730" "10730" "10730"
# no mapping to entrez id
lengthwhichis.na(g_ids)))
[1] 1165
• 2,013 views
•
link
written
by
shinobee •
1 answer
They use another function like:
ae.annots <- AnnotationDbi::select(
x = hgu133a.db,
keys = rownames(data),
columns = "ENTREZID",
keytype = "PROBEID"
)
But still we encounter the problems, I mentioned:
One probe ID to many Entrez ID mapping
sort(table(ae.annots$ENTREZID),decreasing = T)[1:3]
3500 3507 3493
36 32 22
and no mapping at all.
sumis.na(ae.annots$ENTREZID))
[1] 1165
• 0 views
•
link
written
by
shinobee •
Log in to answer this question.
See if this helps: How do I map Affymetrix probe IDs to gene symbols in R? (check the linked Blog page therein).