Map > Problem Definition > Data Preparation > SNP
 

Data Preparation - SNP

A In molecular biology, SNP array is a type of DNA microarray which is used to detect polymorphisms within a population. A single nucleotide polymorphism, a variation at a single site in DNA, is the most frequent type of variation in the genome.
 
GSE6574
Mapping autism risk loci using genetic linkage and chromosomal rearrangements. This experiment's data can be downloaded using the following R code:
library(GEOquery)

# Experiment
dataset.id <- "GSE6754"
gse <- getGEO(dataset.id , GSEMatrix = TRUE)[[1]]
mat <- exprs(gse)
target <- pData(gse)
genes <- featureNames(gse)

# Samples
fname <- paste("c:\\temp\\" , dataset.id , "_targets.csv",sep="")
write.csv(target, file=fname, row.names=FALSE, quote=FALSE)

# Expressions
fname <- paste("c:\\temp\\" , dataset.id , "_expr.csv",sep="")
write.csv(mat, file=fname, row.names=TRUE, quote=FALSE)

# Probes
fname <- paste("c:\\temp\\" , dataset.id , "_probes.csv",sep="")
write.csv(genes,file=fname,row.names=TRUE,quote=FALSE)

# Expressions plot
boxplot(mat[,1:20])
 
Data Processing 
In order to follow one universal data model we create the following three files. Click on the file name to download the file.

 

Bioada SmartArray 
This video shows how you can upload the GSE6754 files to Bioada SmartArray and explore, visualize and build predictive models significantly faster and easier.