Integrated analysis of DNA copy number and gene expression microarray data using gene sets

Background: Genes that play an important role in tumorigenesis are expected to show association between DNA copy number and RNA expression. Optimal power to find such associations can only be achieved if analysing copy number and gene expression jointly. Furthermore, some copy number changes extend over larger chromosomal regions affecting the expression levels of multiple resident genes.

CLEANLOG: Stata module to clean log files

cleanlog takes a plain text or SMCL log file as input and writes a new log file cleaned of all command syntax. It also removes some extraneous material such as the lines of dots displayed for entertainment purposes by programs like bootstrap.log files

MRDUM: Stata module to create dummy variables and summary table for multiple response data

mrdum searches across varlist for integer codes and creates corresponding dummy variables. Each dummy is equal to 1 if the integer code was found anywhere in varlist, 0 if not, and missing if all of varlist is missing. It also displays a table summarizing the results. This program was created specifically to deal with survey questions wherein the respondent can give multiple responses to a single question (e.g. "Check all that apply"). Sometimes these data are coded as a series of variables with the responses entered in the order that the respondent indicated them. Often, however, it is useful to have instead a set of dummy variables that indicate whether the respondent indicated a particular response regardless of the order in which it was indicated.questionnaires, dummy variables, responses