Expression data (available at GEO, accession GSE20403) was normalized using the RMA package within the Affymetrix Expression Console software and annotated.
The data were imported from.CEL files using the Affy package (R/Bioconductor), and the rma statistic was generated for the probe-sets using the rma package (R/Bioconductor).
Mouse data for postpartum testis development (GEO repository: GSE12769) and isolated testicular cells [ 19](ArrayExpress repository: E-TABM-130) were downloaded and pre-processed using the RMA normalization module with AMEN software.
CEL files were processed and normalized using the rma function in the "affy" package of R Bioconductor.
Microarray data were preprocessed using the rma function from the R package "affy".
Normalization and background correction were performed using the rma algorithm of the affy package [ 42].
The data were analysed with the Partek Genomics Suite 6.4 software (Partek Incorporated, U.S). using the RMA (Robust Multi-Array) algorithm.
The expression data were summarized on background-corrected and quantile-normalized data using the RMA algorithm implemented in the Affymetrix Expression Console 1.1 software.
The raw data were processed using R package affy and normalized using the RMA method 25.
Cluster analysis was performed using the MeV software from the TM4 microarray software suite using the default settings (Euclidean distance, and a maximum of 50 iterations), using the RMA normalized expression values from all 12 samples (3 replicates for each of the four treatments) [60].
Normalization was carried out using the RMA algorithm [44] as implemented in Bioconductor.
