MiSummarize {MiDA}

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".

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).

Value

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

Author(s)

Elena N. Filatova

Examples

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]