Analysis Report

Sample

Treatment Group

H1.CEL Treated A

H2.CEL Treated A

H3.CEL Treated A

H4.CEL Treated A

H5.CEL Treated B

H6.CEL Treated B

H7.CEL Treated B

H8.CEL Treated B

H9.CEL Control A

H10.CEL Control A

H11.CEL Control A

H12.CEL Control A

H13.CEL Control B

H14.CEL Control B

H15.CEL Control B

H16.CEL Control B

Data Preprocessing

All data processing was done using Bioconductor or APT tools
The offset of 1 was added to the origianl value before taking the log2
'normgene' and 'control' genes were removed
Endpoint: data matrix of 876 genes X 16 samples
Download Processed Data

Quality Assessment

Quality Assessment Report includes the following figures: Intensity Distribution, Mean Signal, BAC Spike, polya Spike, Pos Vs Neg Auc, Mad Residual Signal, RLE MEAN, and Hierarchical Clustering of Samples plots

Filtering

Probes with log2 intensity < 4 in more than 14 arrays are considered uninformative and removed
Probes with IQR < 10 % are considered uninformative and removed
After filtering: 763 probesets are left
Download Filtered Data

Identification of Differentially Expressed Genes

mainEffect	Comparison	Adjusting	Ratio	P	MultCompAdjtmt	StatMethod	Results
Treatment	Treated vs. Control	none	log2(1.5)	0.05	none	limma	24 genes
Treatment	Treated vs. Control	Group	log2(1.5)	0.05	none	limma	25 genes

Treatment-X-Group

Comparison	Levels	Ratio	P	MultCompAdjtmt	StatMethod	Results
Treatment X Group	none	log2(1.5)	0.05	none	limma	42
Treated vs. Control	A	log2(1.5)	0.05	none	limma	0
Treated vs. Control	B	log2(1.5)	0.05	none	limma	0