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 |