Normalize CEL files with RMAExpress
Convert CEL files to normalized text tables
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.
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/
Convert CEL dataThe user locates the CEL folder and the CDF file.
The RMA conversion is operated with user-selected options, leading to the activation of new menu items
The log-tansformed results are saved to file for use with other programs
Plot normalized data
A number of QC plots are produced to inspect the normalized data
Convert data with the Convertor tool
The companion tool RMA convertor allows direct batch conversion without QC plots.
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