illuminaHumanv2.db returning NA for all Illumina probe ID to gene symbol conversion
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12 months ago
accibio ▴ 20

I have cross-posted this question on Stack Bioinformatics. I'll put an update if the question is answered there.

I have downloaded a miRNA expression dataset from NCBI GEO (GSE25631) to study differential gene expression and perform other analyses. As mentioned in GEO, this profiling was performed on GPL8179 Illumina Human v2 MicroRNA expression beadchip. Accordingly, I installed the illuminaHumanv2.db package to annotate the Illumina probe IDs. However, when I tried to convert the Illumina probe IDs to their corresponding gene symbols, it returned NA for all the probes. Can anybody identify the issue with this approach? Here's the R script which I used.

library(GEOquery)
library(limma)
library(illuminaHumanv2.db)

Sys.setenv(VROOM_CONNECTION_SIZE = 256000)

data <- getGEO(GEO = "GSE25631", 
           destdir = "E:\\GSE25631",
           GSEMatrix = TRUE,
           AnnotGPL = FALSE,
           getGPL = FALSE,
           parseCharacteristics = TRUE)

data <- data$GSE25631_series_matrix.txt.gz

raw_intensity <- exprs(data)

samples <- as.character(pData(data)[,"title"])

raw_intensity_log <- log2(raw_intensity)
colnames(raw_intensity_log) <- c(rep("GBM", 82), rep("Normal", 5))

probe_id <- rownames(raw_intensity_log)
mapping <- data.frame(Gene = unlist(mget(x = probe_id, envir = illuminaHumanv2SYMBOL, ifnotfound = NA)))



head(mapping, 10)
               Gene
ILMN_3166935   NA
ILMN_3166938   NA 
ILMN_3166940   NA
ILMN_3166941   NA 
ILMN_3166943   NA
ILMN_3166944   NA
ILMN_3166945   NA
ILMN_3166948   NA
ILMN_3166952   NA
ILMN_3166953   NA

The GSE25631_RAW.tar file in the supplementary section has all the Probe ID to Gene mappings but I'm curious to know why this approach didn't work.

microarray illumina R probe-annotation • 633 views
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