getEDB {maDB}R Documentation

Retrieving expression values from a database.

Description

getEDB retrieves expression values from the specified signal channels from a maDB database. For further informations and examples refer to the package vignette (which can be opened using the openMadbVignette).

Usage

getEDB(con,ids,signal.channels.pk,column.names=c("array_name","color"),v=TRUE)

Arguments

con The connection to the database (created with the dbConnect function from the RdbiPgSQL package).
ids The IDs of the genes from which the expression values should be retrieved. In the case of Affymetrix GeneChips the Affymetrix IDs should be used (as they are used as rownames in the exprs matrix in the ExpressionSet objects).
signal.channels.pk the primary keys of the signal channels in the database from which the expression values should be retrieved. To get information about primary keys, arrays... from the database use the dbGetExperimentInfo function.
column.names The information that should be used as column names of the expression values matrix. Allowed are all column names of the sample database table.
v If TRUE additional information will be printed to the console.

Details

This function is useful, to retrieve only a subset of genes from a subset of signal channels of a microarray experiment (dataset) from a maDB database.

Author(s)

Johannes Rainer

See Also

publishToDB dbGetExperimentInfo loadFromDB getMDB


[Package maDB version 1.12.0 Index]