MiDA (version 0.1.2)

MiSummarize: Microarray data summarization

Description

Counts median of intensities for multiple probes that target one gene/transcript.

Usage

MiSummarize(Matrix, sep, method = "median")

Arguments

Matrix

numeric matrix of intensities data where each row corresponds to a probe (gene, transcript), and each column correspondes to a specimen (patient). Row names of Matrix should contain probe IDs that consist of three terms: gene name - transcript name - probe name.

sep

a character string to separate the terms in probe IDs.

method

character string specifying summarization method. Possible values are "median" and "mean".

Value

gene/transcript expression matrix with median/mean of expression intensities for each gene/transcript.

Details

This function is used for summarizing expression intensities data when multiple probes target one gene/transcript. Row names of Matrix should contain probe IDs that consist of 3 terms: "Gene name - sep - transcript name - sep - probe name" (for example, "AGTR2.ALL" - for gene, only one probe; "AGTR2.NM_000686.z1" - 1st probe to AGTR2 NM_000686 mRNA transcript).

Examples

# NOT RUN {
data("IMexpression") # load data
# See 5 zonds to AGTR2.NM_000686
IMexpression [1:10, 1:5]
SumMatrix<-MiSummarize(IMexpression, sep=".")
# now there is median expression for AGTR2.NM_000686
SumMatrix[ 1:10, 1:5]

# }