Normalize CEL files with RMAExpress

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Convert CEL files to normalized text tables

rmaexpress_logo.png

[ Main_Page | Hands-on Analysis of public microarray datasets ]

Introduction

Many programs, like CLC require normalized microarray data as input and do not support the CEL format. RMA_eXpress and its companion convertor tool rapidely produce normalized and log-transformed data from a collection of CEL files and the corresponding CDF annotation database and without the need to install R and bioconductor packages.

RMA eXpress was cited in several publications (eg [1]) and is available for Windows AND for mac OSX from its developer site [2]. A manual is also available here

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The Affymetrix tools produce the same kind of data with more QC plots and are preferred if you want to have a close look to your data

RMAeXpress run with the GSE6943 data

In order to perform this exercise, please first install the software (v1.1.0) from the following link: http://rmaexpress.bmbolstad.com/

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You will need the rat RAE230A.CDF file accessible from the link at the bottom of this page

Convert CEL data

The user locates the CEL folder and the CDF file.

Technical.png obviously all CEL files should come from the same CHIP


RMA_eXpress_01.png


RMA_eXpress_02.png

The RMA conversion is operated with user-selected options, leading to the activation of new menu items


RMA_eXpress_03.png


RMA_eXpress_04.png

The log-tansformed results are saved to file for use with other programs


RMA_eXpress_05.png

Plot normalized data

A number of QC plots are produced to inspect the normalized data


RMA_eXpress_06.png


RMA_eXpress_07.png


RMA_eXpress_08.png

Convert data with the Convertor tool

The companion tool RMA convertor allows direct batch conversion without QC plots.


RMA_convert_01.png

Final result

The resulting data for the GSE experiment is shown below (top 5 lines by first 5 columns for readability) 

Probesets   GSM160089.CEL  GSM160090.CEL  GSM160091.CEL  GSM160092.CEL
1367452_at  9.642959       9.651789       9.328636       9.484756
1367453_at  10.155364      10.249902      10.186186      10.096563
1367454_at  8.739058       9.082530       9.071610       8.687629
1367455_at  10.476362      10.447124      10.571050      10.326480

download exercise files

Download exercise files here.

Use the right application to open the files present in RMAeXpress-files


References:
  1. ↑

    Claudia Mimoso, Ding-Dar Lee, Jiri Zavadil, Marjana Tomic-Canic, Miroslav Blumenberg
    Analysis and meta-analysis of transcriptional profiling in human epidermis.
    Methods Mol Biol: 2014, 1195;61-97
    [PubMed:24297317] ##WORLDCAT## [DOI] (I p)

    Małgorzata Janas-Kozik, Urszula Mazurek, Irena Krupka-Matuszczyk, Małgorzata Stachowicz, Joanna Głogowska-Ligus, Tadeusz Wilczok
    The transcript expression profile of the leptin receptor-coding gene assayed with the oligonucleotide microarray technique--could this be an anorexia nervosa marker?
    Cell Mol Biol Lett: 2006, 11(1);62-9
    [PubMed:16847749] ##WORLDCAT## [DOI] (I p)

    Yoseph Barash, Elinor Dehan, Meir Krupsky, Wilbur Franklin, Marc Geraci, Nir Friedman, Naftali Kaminski
    Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays.
    Bioinformatics: 2004, 20(6);839-46
    [PubMed:14751998] ##WORLDCAT## [DOI] (P p)

  2. ↑ http://rmaexpress.bmbolstad.com/

[ Main_Page | Hands-on Analysis of public microarray datasets ]

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