2. Expression Data Analysis

Sample Information 6 assays
Data Analysis Performed by Ricky Lim (Benoukraf’s Lab)
Date Data Received 5th June, 2015

2.1 Data Normalization


The input raw expression data in IDAT format, annotation file, and sampleSheet are available for download here as a zip file.


Raw Illumina BeadArray data in IDAT format were preprocessed with bgxFile, containaining the array design information from Illumina, GPL6887_MouseWG-6_V2_0_R3_11278593_A.txt.gz .using an open-source Bioconductor package illuminaio (PMID:24701342). the bgx file was downloaded from NCBI, GEO accession: GPL6887.

Following the preprocessing, the expression data were normalized by applying control background correction, log transformation and inter-quantile normalization using limma bioconductor package neqc function. (PMID:25605792) and the normalized expression data were annotated from GPL6887_MouseWG-6_V2_0_R3_11278593_A.txt.gz for probes only

Full Normalization procedures and codes (pdf format) can be downloaded here.
Normalized data matrix (txt format with tab separator) can be downloaded here (right click and download target as).