GAR_PA_2015_001_GeneExpressionMethylation


2. Expression Data Analysis

Sample Information 6 assays x 4 replicates
Experiment Performed by Tan Sili (Soong’s Lab)
Data Analysis Performed by Ricky Lim (Benoukraf’s Lab)
Date Data Received 23th June, 2015

2.1 Data Normalization

The raw expression data was loaded using affy bioconductor and normalized using rma (robust multi-array average) function.

Following the normalization, the normalized expression data was annotated based on their probe ids for entrez symbols and entrez ids using databases downloaded from bioconductor library("hugene10stv1cdf"), library("hugene10stv1probe"), library("hugene10stprobeset.db"), library("hugene10sttranscriptcluster.db")

Full Normalization procedures and codes (pdf format) can be downloaded here.
The input raw expression data in CEL format is available for download here as a zip file.
Normalized data matrix (txt format with tab separator) can be downloaded here (right click and download target as).

3. Methylation Data Analysis

Sample Information 6 assays x 4 replicates
Experiment Performed by Tan Sili (Soong’s Lab)
Data Analysis Performed by Ricky Lim (Benoukraf’s Lab)
Date Data Received 23th June, 2015

3.1 Data Normalization

The raw expression data was loaded using minfi bioconductor and normalized using preprocessSWAN (SWAN, Subset Quantile within Array, normalization) function.

Following the normalization, the normalized methylation data was extracted into B and M scores.

Full Normalization procedures and codes (pdf format) can be downloaded here.
The input raw expression data in IDAT format is available for download here as a zip file.
Normalized Beta score(txt format with tab separator) can be downloaded here (right click and download target as). This zip file contains a file for beta score for each sample assayed in this study
Normalized M score(txt format with tab separator) can be downloaded here (right click and download target as). This zip file contains a file for M score for each sample assayed in this study