1. Differential Analysis & FDR Correction
Much more effective than only looking at P-values. 1

2. Correlation Analysis Steps
Step 1: Construction of input data table in EXCEL
Step 2: Save EXCEL file into tab delimited txt file
Step 3: Upload data - tab delimited txt file
Step 4: Choose correlation algorithm
Step 5: Enter your and submit
Step 6: Result interpretation: global FDR
Step 7: Result interpretation: local FDR
Correlation Analysis Steps

3. Construction of input data
Step 1:
Construction of input data
table in EXCEL
Sample
Clinical parameter
Gene
patient.1.name …
patient.2.name

4. Step 1: Input data format: Cell A1: “sample”
1st Column: patient names or IDs
1st Row: .
Cell A2: clinical parameter
Cell A3 & others: gene name
2nd column: values of one clinical parameter
All other cells should be molecular data,
one sample/patient per row
e.g. array intensity or protein quantities

5. EXCEL file example

6. Step 2: Save EXCEL file into tab delimited txt file

7. Step 3: Upload data - tab delimited txt file1 2 3

8. Step 3: Upload data - tab delimited txt file
Input data “input.cor.txt” selected

9. Step 4: Choose algorithm for correlation analysis
Choose correlation algorithm

10. Step 4: which one to choose?
Rank based correlation – study relationship between different rankings on the same set of items
During the analysis, raw scores are converted to rankings
Spearman
Kendall
Pearson product-moment correlation coefficient

11. To correlate a clinical variable to molecular data: Spearman’s rank, Kendall tau, or Pearson product-moment correlation coefficient analysis?
Spearman’s Rank Correlation Coefficient Analysis:
Spearman rank correlation is used when you have two measurement variables and one “hidden” nominal variable, which groups the measurements into pairs. It is a non-parametric test for correlation and used when one or both of the variables consists of ranks.
Kendall Tau Correlation Coefficient Analysis:
Kendall's Tau Correlation Coefficient analysis is a measure of correlation and measures the strength of the relationship between two variables. It provides a distribution free test of independence and a measure of the strength of dependence between two variables. It is required two variables, X and Y, that are paired observations. Both variables that are provided should be at least ordinal.
Pearson Product-Moment Correlation Coefficient Analysis:
The Pearson product-moment correlation coefficient is a common measure of the correlation (linear dependence) between two variables X and Y. It is very widely used in the sciences as a measure of the strength of linear dependence between two variables, giving a value somewhere between +1 and -1 inclusive.

12. Step 5: Enter your email and submit

13. Step 6: Result interpretation Global FDR
Single hypothesis test
= correlation between one gene and one clinical variable

14. Step 6: Result interpretation Global FDR
FDR plot red line:
Total Discoveries (TD) or Total Discovery rate = 1
FDR plot green line:
False Discoveries (MEAN) or False Discovery Rate FDR (MEAN)
FDR plot black bar line:
False Discoveries (MEDIAN) or False Discovery Rate FDR (MEDIAN)
FDR plot blue line:
False Discoveries (95%) or False Discovery Rate FDR (95%)
FDR plot dotted black line:
FDR=0.05

15. Step 6: Result interpretation Global FDR

16. Step 6: How to read the gFDR plots
Commonly used global FDR cut off
0.05
If there are no significant features
No data points will show up below
the 0.05 dotted horizontal line

17. Step 6: Result interpretation Global FDR
Commonly used
gFDR cutoff: 0.05
Features which satisfy global FDR < 0.05

18. Step 6: Result interpretation Global FDR
Commonly used
gFDR cutoff: 0.05
Features which satisfy global FDR < 0.05

19. Step 7: Result interpretation local FDR

20. Step 7: How to read the lFDR plots
It has been suggested (Aubert, et al., 2004) that the first abrupt change of the local FDR can be an indication for the determination of a good threshold to choose genuinely statistically significant features.

21. Step 7: Result interpretation local FDR
1st abrupt change of lFDR

22. Step 7: Result interpretation local FDR
Click to download result file

23. Step 7: Result interpretation local FDR
Local FDR results:
1st column: feature name
2nd column: correlation test P value
3rd column: local FDR results