RMAExpress

Written by Ben Bolstad
email bmb@bmbolstad.com

What is RMAExpress?

RMAExpress is a standalone GUI program for Windows, OS X and Linux to compute gene expression summary values for Affymetrix Genechip® data using the Robust Multichip Average expression summary and to carry out quality assessment using probe-level metrics. It does not require R nor is it dependent on any component of the BioConductor project. If focuses on processing 3' IVT expression arrays, exon and WT gene arrays.

What is RMA?

RMA is the Robust Multichip Average. It consists of three steps: a background adjustment, quantile normalization (see the Bolstad et al reference) and finally summarization. Some references (currently published) for the RMA methodology are:
Bolstad, B.M., Irizarry R. A., Astrand, M., and Speed, T.P. (2003), A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. Bioinformatics 19(2):185-193 Supplemental information
Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, Bridget Hobbs and Terence P. Speed (2003), Summaries of Affymetrix GeneChip probe level data Nucleic Acids Research 31(4):e15
Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, Antonellis, KJ, Scherf, U, Speed, TP (2002) Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Accepted for publication in Biostatistics. [Abstract, PDF, PS, Complementary Color Figures-PDF, Software]

What do I need?

You will need the appropriate CDF and CEL files for your dataset.

For Exon and WT Gene arrays, the PGF and CLF should be used instead of the CDF file to build a CDFRME file. The process for doing this is explained in the user manual. Some pre-built CDFRME files are also available.
CDFRME files
HuEx_CDFRME.zip (95.9MB)
HuGene_CDFRME.zip (5.5MB)
HuGene1.1_CDFRME.zip (10MB)
MoEx_CDFRME.zip (79.6MB)
MoGene_CDFRME.zip (6.3MB)
MoGene1.1_CDFRME.zip (6.3MB)
RaEx_CDFRME.zip (48.4MB)
RaGene_CDFRME.zip (5.7MB)

Can I use affy/BioConductor instead?

Of course. Hypothetically you will get the same results from both places, provided you have consistent settings in affy/BioConductor and RMAExpress. Some people prefer the power and flexibility of R and others like the point and click simplicity of a GUI. RMAExpress caters to the second option. Since RMAExpress outputs the computed expression values to a text file, you may of course load the expression measures into R and use features of Bioconductor for the analysis of your gene expression values. You can of course open the results file in any other application that supports importing plain text files.

Will I get the same results as I would using affy/Bioconductor?

Yes. The results from RMAExpress should be consistent.

What are the machine requirements?

A good rule of thumb is the more RAM you have the better. I would recommend at least 1GB, though 512MB will work in most situations.

At this point the program has been tested using Windows 2000, Windows XP, Windows Vista and Linux.

Most recently I have had a report of over 10,000 arrays processed in a single session.

Can I do any quality assessment?

Yes, store the residuals when you compute the expression values. Then you may examine chip pseudo-images of the residuals. Note that high positive residuals are colored increasingly read and low negative residuals are colored increasingly blue.

To better interpret these images and gain a better feel for what is typical you may visit the PLM Image Gallery where images for a number of different datasets are shown.

Access to the NUSE and RLE quality assessment metrics is also provided.

How do I download and install it?

Click here for the current release Windows version. Use the installer to install the program. The current release version number is 1.1.0 (released August 7, 2014). A pre-built linux version is not currently available, but you may build it using the source code. You can download pre-release versions from the following table (the release versions will be more stable, the development versions may have features that are incomplete or will be removed or altered before the next release version),

VersionDate
1.0.5 Release (Windows)
1.0.5 Release (Mac OS X)
May 22, 2010
1.1.0 (Windows)
1.1.0 (Mac OS X)
Aug 7, 2014

Screenshots

Screenshot of RMAExpress on Windows XP

Screenshot of RMAExpress on Windows XP

Screenshot of RMAExpress on Linux

Is there a mailing list?

Yes. You may subscribe by sending email to rmaexpress_help-request@freelists.org with 'subscribe' in the Subject field or unsuscribe by sending email to the same address with 'unsubscribe'. Once you are a member you may send messages to the list by sending an email to rmaexpress_help@freelists.org. The archive is available here.

I just want expression estimates. What do I do?

In most cases you do not need to use the RMADataConv program. You should just read in your data directly into RMAExpress using the "Read Unprocessed files" option. It will ask you for the locations of your CDF and CEL files, then read the data. Next select "Compute RMA measure" to actually compute the expression measure. It will bring a dialog box up asking you to select specific options (just leave the defaults), press ok and it will compute RMA expression summaries. Then choose "Write results to file" to output the expression summaries to a text file.

Is there a user manual or other documentation?

Yes. It is included in the installation as a PDF file. You may download the latest release version of the RMAExpress Users Guide separately.

Can I get the source code?

Yes. The source code is available under the GNU Public License Version 2. To understand the GPL read the GPL FAQ.

You can download the source code for RMAExpress_1.0.5_src.tar.gz which is the current release version. Note to build it you will require the wxWidgets library. The code should build on both Windows and Linux. I will not support pre-built binaries except those available from this website. Source code stating with the 1.1.0 series is hosted on github and may be found here: RMAExpress source releases

You can find instructions for building RMAExpress here (these may be outdated). Note that most people will not want to compile the source code themselves, but instead just use the pre-built binaries. A brief changelog is also available.

Is there a version for Mac OS X?

Yes. See the download table above. Mac OS X versions start with 1.0.5 Release.

Questions/Comments/Problems/Feature Requests?

Send me an email at bmb@bmbolstad.com.