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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