differential analysis & fdr correction
DESCRIPTION
Differential Analysis & FDR Correction. Differential 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 T or U Test Step 5: Enter your email and submit - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/1.jpg)
Differential Analysis& FDR Correction
![Page 2: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/2.jpg)
Differential Analysis Steps
Step 1: Construction of input data table in EXCELStep 2: Save EXCEL file into tab delimited txt fileStep 3: Upload data - tab delimited txt fileStep 4: Choose T or U Test Step 5: Enter your email and submitStep 6: Result interpretation: global FDRStep 7: Result interpretation: local FDR
![Page 3: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/3.jpg)
Step 1:
CLASS 1 1 0 0
Gene.1.name … … … …
Gene.2.name … … … …
… … … … …
… … … … …
Construction of input data table in EXCEL
![Page 4: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/4.jpg)
Step 1:
CLASS 1 1 0 0
Gene.1.name … … … …
Gene.2.name … … … …
… … … … …
… … … … …
Input data format:• Cell A1: “CLASS”• 1st Column: feature names• 1st Row: sample categories.
• It has to be binary, either 1 or 0• e.g. 1 is disease, 0 is control
• All other cells should be data, one sample per one column• e.g. array intensity or protein quantities
![Page 5: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/5.jpg)
EXCEL file example
![Page 6: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/6.jpg)
Step 2: Save EXCEL file into tab delimited txt file
![Page 7: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/7.jpg)
Step 3: Upload data - tab delimited txt file
1
2
3
![Page 8: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/8.jpg)
Step 3: Upload data - tab delimited txt file
Input data “input.txt” selected
![Page 9: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/9.jpg)
Step 4: Choose T test or U test
Choose either T or U test for analysis
![Page 10: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/10.jpg)
Step 4: T test or U test, which one to choose?
• The U test is useful in the same situations as t test
• U test should be used if the data are ordinal
• U test is more robust to outliers
• U test is more efficient • For distribution far from normal and for sufficiently large samples
![Page 11: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/11.jpg)
To Discover Differential Features: Student’s T test or Mann Whitney U test?
Student’s T test:
Student’s T test is a parametric test of the null hypothesis, where the means of 2 normally distributed populations are equal. It is used when you have a nominal variable, which must only have 2 values, such as “male” and “female,” and measurement variable, and you want to compare the mean values of the measurement variable. It is a test of the null hypothesis, where the means of 2 normally distributed populations are equal.
Mann-Whitney U Test: Mann-Whitney U Test is a non-parametric test that examines whether 2 sites of
data could have come from the same population. It requires 2 data sets that do not need to be paired, normally distributed, or have equal numbers in each set.
![Page 12: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/12.jpg)
Step 5: Enter your email and submit
Enter your email
Submit
![Page 13: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/13.jpg)
Step 6: Result interpretationGlobal 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
![Page 14: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/14.jpg)
95% FD/TD .05 FDR1 = TD/TD
Single hypothesis test P-value thresholds
Mean FD/TD Median FD/TDA
Glo
bal
FD
R0.
00.
20.
40.
60.
81.
0
0.0
0.2
0.4
0.6
10-9 0.01 0.02 0.03 0.0410-9 0.05 1.0
Step 6: Result interpretationGlobal FDR
![Page 15: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/15.jpg)
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
![Page 16: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/16.jpg)
95% FD/TD .05 FDR1 = TD/TD
Single hypothesis test P-value thresholds
Mean FD/TD Median FD/TDA
Glo
bal
FD
R0.
00.
20.
40.
60.
81.
0
0.0
0.2
0.4
0.6
10-9 0.01 0.02 0.03 0.0410-9 0.05 1.0
Step 6: Result interpretationGlobal FDR
Features which satisfy global FDR < 0.05
Commonly used gFDR cutoff: 0.05
![Page 17: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/17.jpg)
95% FD/TD .05 FDR1 = TD/TD
Single hypothesis test P-value thresholds
Mean FD/TD Median FD/TDAG
lob
al
FD
R0.
00.
20.
40.
60.
81.
0
0.0
0.2
0.4
0.6
10-9 0.01 0.02 0.03 0.0410-9 0.05 1.0
Step 6: Result interpretationGlobal FDR
95% FD/TD .05 FDR1 = TD/TD
Single hypothesis test P-value thresholds
Mean FD/TD Median FD/TDA
Glo
bal
FD
R0.
00.
20.
40.
60.
81.
0
0.0
0.2
0.4
0.6
10-9 0.01 0.02 0.03 0.0410-9 0.05 1.0
Features which satisfy global FDR < 0.05
Commonly used gFDR cutoff: 0.05
![Page 18: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/18.jpg)
Step 7: Result interpretationlocal FDR
Lo
cal F
DR
Single hypothesis test P-value
0.0 0.01 0.02 0.03 0.04 0.050.0 0.2 0.4 0.6 0.8 1.0
0.0
0.2
0.4
0.6
0.8
1.0
0.0
0.0
50
.10
0.1
50
.20
![Page 19: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/19.jpg)
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.
![Page 20: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/20.jpg)
Step 7: Result interpretationlocal FDR
Lo
cal F
DR
Single hypothesis test P-value
0.0 0.01 0.02 0.03 0.04 0.050.0 0.2 0.4 0.6 0.8 1.0
0.0
0.2
0.4
0.6
0.8
1.0
0.0
0.0
50
.10
0.1
50
.20
1st abrupt change of lFDR
![Page 21: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/21.jpg)
Step 7: Result interpretationlocal FDR
Click to download result file
![Page 22: Differential Analysis & FDR Correction](https://reader036.vdocuments.net/reader036/viewer/2022062322/56814547550346895db21511/html5/thumbnails/22.jpg)
Step 7: Result interpretationlocal FDR
Local FDR results:• 1st column: feature name
• 2nd column: t or U test P value
• 3rd column: local FDR results