getMDB {maDB}R Documentation

Retrieving regulation values from a database.

Description

getMDB this function reads the regulation (M) values from the selected comparisons out of a PostgreSQL database. Micro array experiments can be stored into a PostgreSQL database using the publishToDB method of the EexprSet object. The corresponding regulation values can then be calculated with the calculateDBRegulations function.

Usage

getMDB(con,ids=NULL,comparisons.pk=NULL,v=TRUE,column.names="description")

Arguments

con A connection object (create it with the dbConnect.PgSQL.conn function from the package RdbiPgSQL)
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 exprSet objects).
comparisons.pk the primary keys of the comparisons in the database from which the regulation values should be retrieved. To get all available comparisons from the database call dbGetResult(dbSendQuery(con,"SELECT * FROM comparisons")), where con is the database connection object and the column comparisons\_pk contains the primary keys. This SQL call can be extended to the samples that are hybridized in the signal channel used as “red” signal channel (M = log2( R / G)): dbGetResult(dbSendQuery(con,"SELECT * FROM comparisons JOIN signal\_channels ON (red\_signal\_channel=signal\_channels\_pk) JOIN samples ON (samples\_fk=samples\_pk)")). By switching the “red_signal_channel” with “green_signal_channel” the call retrieves the same information, but with information about the green signal channel (usually the control sample).
column.names The information that should be used as column names of the returned regulation values matrix. Allowed are all column names of the sample and comparisons database tables.
v If TRUE additional information will be printed to the console.

Details

This function is useful, if one wants to get regulation values of a set of genes in a set of comparisons.

Author(s)

Johannes Rainer

References

See Also

publishToDB dbGetExperimentInfo dbConnect loadFromDB getEDB


[Package maDB version 1.2.0 Index]