Free Knowledge Resources


Linux Manual Pages


Free Software * Books

Source Code

Free Media

Linux

rsem-control-fdr(1)


NAME

   rsem-control-fdr

PURPOSE

   Filter EBSeq output for statistical significance.

SYNOPSIS

   rsem-control-fdr [options] input_file fdr_rate output_file

ARGUMENTS

   input_file
       This should be the main result file generated by 'rsem-run-ebseq',
       which contains all genes/transcripts and their associated
       statistics.

   fdr_rate
       The desire false discovery rate (FDR).

   output_file
       This file is a subset of the 'input_file'. It only contains the
       genes/transcripts called as differentially expressed (DE). When
       more than 2 conditions exist, DE is defined as not all conditions
       are equally expressed.  Because statistical significance does not
       necessarily mean biological significance, users should also refer
       to the fold changes to decide which genes/transcripts are
       biologically significant. When more than two conditions exist, this
       file will not contain fold change information and users need to
       calculate it from 'input_file.condmeans' by themselves.

OPTIONS

   --hard-threshold
       Use hard threshold method to control FDR. If this option is set,
       only those genes/transcripts with their PPDE >= 1 - fdr_rate are
       called as DE. (Default: on)

   --soft-threshold
       Use soft threshold method to control FDR. If this option is set,
       this program will try to report as many genes/transcripts as
       possible, as long as their average PPDE >= 1 - fdr_rate. This
       option is equivalent to use EBSeq's 'crit_fun' for FDR control.
       (Default: off)

   -h/--help
       Show help information.

DESCRIPTION

   This program controls the false discovery rate and reports
   differentially expressed genes/transcripts.

EXAMPLES

   We assume that we have 'GeneMat.results' as input. We want to control
   FDR at 0.05 using hard threshold method and name the output file as
   'GeneMat.de.txt':

    rsem-control-fdr GeneMat.results 0.05 GeneMat.de.txt



Opportunity


Personal Opportunity - Free software gives you access to billions of dollars of software at no cost. Use this software for your business, personal use or to develop a profitable skill. Access to source code provides access to a level of capabilities/information that companies protect though copyrights. Open source is a core component of the Internet and it is available to you. Leverage the billions of dollars in resources and capabilities to build a career, establish a business or change the world. The potential is endless for those who understand the opportunity.

Business Opportunity - Goldman Sachs, IBM and countless large corporations are leveraging open source to reduce costs, develop products and increase their bottom lines. Learn what these companies know about open source and how open source can give you the advantage.



Free Software


Free Software provides computer programs and capabilities at no cost but more importantly, it provides the freedom to run, edit, contribute to, and share the software. The importance of free software is a matter of access, not price. Software at no cost is a benefit but ownership rights to the software and source code is far more significant.

Free Office Software - The Libre Office suite provides top desktop productivity tools for free. This includes, a word processor, spreadsheet, presentation engine, drawing and flowcharting, database and math applications. Libre Office is available for Linux or Windows.



Free Books


The Free Books Library is a collection of thousands of the most popular public domain books in an online readable format. The collection includes great classical literature and more recent works where the U.S. copyright has expired. These books are yours to read and use without restrictions.

Source Code - Want to change a program or know how it works? Open Source provides the source code for its programs so that anyone can use, modify or learn how to write those programs themselves. Visit the GNU source code repositories to download the source.



Education


Study at Harvard, Stanford or MIT - Open edX provides free online courses from Harvard, MIT, Columbia, UC Berkeley and other top Universities. Hundreds of courses for almost all major subjects and course levels. Open edx also offers some paid courses and selected certifications.

Linux Manual Pages - A man or manual page is a form of software documentation found on Linux/Unix operating systems. Topics covered include computer programs (including library and system calls), formal standards and conventions, and even abstract concepts.


birds banner