In v1.5, DEG module function is greatly improved. The Wilcoxon rank sum test, which is the nonparametric test that is useful for analyzing the 2 group data (not related with normal distribution) and Wilcoxon singed rank test are added. The newly added correlation plot enables the user to understand the correlation between the samples visually with the selected Differentially Expressed Gene.
Also various user¡¯s convenience functions are improved such as folder renaming etc. The Pathway search function has improved and it searches the provided group of the Differentially Expressed Gene or the KEGG pathway common to gene cluster and also indicates the corresponding genes on the pathway (Gene-to-Pathway mapping).
Preprocessing Module- Two-dye data importing: Added ImaGene data format
- Normalization for one-dye case: Added Lowess normalization
- Automatic naming function (Image file name); Able to save all files at once
- Improved Box plot speed
DEG Module- 2-class unpaired test: Added Wilcoxon rank sum test (= Mann-Whitney test)
- 2-class paired test: Added Wilcoxon signed rank test
- Calculate the correlation between the samples with the extracted Differentially Expressed Gene:Correlation Plot function is added in the DEG results window
- Improved Permutation test: iteration number setup, indication of progress rate etc.
- Folder renaming in Project tree: Able to assign beforehand in dialogue box
- Volcano plot: Improved submitted gene mapping
Clustering Module- Column editing: column deletion, column average, column operation (+/-)
- Folder renaming in Project tree
Common point- Gene list save file format: supports *.csv (comma separated value)
- Indicates corresponding genes that are extracted from analyzed results within the KEGG pathway
- Common pathway function: Searches the KEGG pathway that is commonly related to provided genes
- Additional function (Experimental information window): [copy] & [paste]
- Affymetrix GeneChip annotation: Provides NetAffx annotation regarding to all chip models