dbCalculateRegulations {maDB}R Documentation

Calculate regulation values from expression values in the database

Description

dbCalculateRegulations calculates regulation values (M values, log2 fold change values) from expression values retrieved from the database and inserts these regulation values in the according database table (database tables textit{comparisons} and textit{regulation_values}, see the vignette for more information (openMadbVignette)).

Usage

dbCalculateRegulations(Con,exp.title,comparisons,v=TRUE)

Arguments

Con The connection to the database (see dbConnect from the RdbiPgSQL package).
exp.title The tile of the microarray experiment (data set) for which the regulation values should be calculated. Note that it is only possible to calculate regulation values for comparisons of arrays within a microarray experiment, which means that this regulation values can only be calculated for two color arrays or Affymetrix GeneChips which were normalized together.
comparisons A list of comparisons for which M and A values should be calculated. To calculate regulation values for the first three chips of an experiment (comparing the expression values of the features/probe sets of the second signal channel (array) with those of the first (control) and of the third chip to those of the first) submit list(c(2,1),c(3,1)). Use the function dbGetExperimentInfo to get information of the arrays/signal channels of a experiment and the according index of the signal channels in this experiment.
v If TRUE the progress of the calculation is shown using a progress bar.

Details

This function allows to calculate regulation values comparing expression values from two signal channels of a microarray experiment (dataset) in the maDB database. The according comparisons will be inserted into a database table called textit{comparisons} whichs attribute textit{r_signal_channel} links to the signal channel that was used as sample and whichs attribute textit{g_signal_channel} links to the signal channel that was used as control sample. The regulation values are calculated using the formula M=r-g and A=0.5*(r+g) where r and g are the expression values in log2 scale. The regulation values (M and A values) are inserted into a database table called textit{regulation_values}. Regulation values can be fetched from the database using the getMDB function. The function dbGetComparisons can be used to get informations which samples were compared in the comparisons in the database.

Author(s)

Johannes Rainer

See Also

dbGetExperimentInfo dbGetComparisons


[Package maDB version 1.12.0 Index]