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Perform data analysis on Reversed phase POSITIVE ION MODE dataset in study ST002833
Choose experimental groups (required for Volcano plot, OPLSDA, Random Forest analyses)
Select 2 different experimental groups:
Select only groups with 3 or more replicates listed in parentheses
Group1
Genotype:Analytical Blank | Treatment:Method Blank (7)
Genotype:Quality Control | Treatment:Sample Pool (6)
Genotype:bacterial community | Treatment:mGAM fresh (3)
Genotype:bacterial community | Treatment:mGAM spent by Bacteroides fragilis (3)
Genotype:bacterial community | Treatment:mGAM spent by Bacteroides thetaiotaomicron (3)
Genotype:bacterial community | Treatment:mGAM spent by Bacteroides uniformis (3)
Genotype:bacterial community | Treatment:mGAM spent by Blautia producta (3)
Genotype:bacterial community | Treatment:mGAM spent by Clostridium clostridioforme (3)
Genotype:bacterial community | Treatment:mGAM spent by Clostridium hathewayi (3)
Genotype:bacterial community | Treatment:mGAM spent by Clostridium hylemonae (3)
Genotype:bacterial community | Treatment:mGAM spent by Clostridium scindens (3)
Genotype:bacterial community | Treatment:mGAM spent by Clostridium symbiosum (3)
Genotype:bacterial community | Treatment:mGAM spent by Enterococcus faecalis (3)
Genotype:bacterial community | Treatment:mGAM spent by Enterococcus faecium (3)
Genotype:bacterial community | Treatment:mGAM spent by Enterococcus hirae (3)
Genotype:bacterial community | Treatment:mGAM spent by Escherichia fergusonii (3)
Genotype:bacterial community | Treatment:mGAM spent by Flavonifractor plautii (3)
Genotype:bacterial community | Treatment:mGAM spent by Parabacteroides distasonis (3)
Group2
Genotype:Analytical Blank | Treatment:Method Blank (7)
Genotype:Quality Control | Treatment:Sample Pool (6)
Genotype:bacterial community | Treatment:mGAM fresh (3)
Genotype:bacterial community | Treatment:mGAM spent by Bacteroides fragilis (3)
Genotype:bacterial community | Treatment:mGAM spent by Bacteroides thetaiotaomicron (3)
Genotype:bacterial community | Treatment:mGAM spent by Bacteroides uniformis (3)
Genotype:bacterial community | Treatment:mGAM spent by Blautia producta (3)
Genotype:bacterial community | Treatment:mGAM spent by Clostridium clostridioforme (3)
Genotype:bacterial community | Treatment:mGAM spent by Clostridium hathewayi (3)
Genotype:bacterial community | Treatment:mGAM spent by Clostridium hylemonae (3)
Genotype:bacterial community | Treatment:mGAM spent by Clostridium scindens (3)
Genotype:bacterial community | Treatment:mGAM spent by Clostridium symbiosum (3)
Genotype:bacterial community | Treatment:mGAM spent by Enterococcus faecalis (3)
Genotype:bacterial community | Treatment:mGAM spent by Enterococcus faecium (3)
Genotype:bacterial community | Treatment:mGAM spent by Enterococcus hirae (3)
Genotype:bacterial community | Treatment:mGAM spent by Escherichia fergusonii (3)
Genotype:bacterial community | Treatment:mGAM spent by Flavonifractor plautii (3)
Genotype:bacterial community | Treatment:mGAM spent by Parabacteroides distasonis (3)
Filtering Parameters
Select threshold % for selection below:
100% (option 4 only)
95%
90%
85%
80%
75%
70%
65%
60%
55%
50%
45%
40%
35%
30%
20%
10%
0%
Option 1:
Filter by Sum
(Analytes whose sum for all samples falls below the threshold % will be excluded)
Option 2:
Filter by Mean
(Analytes whose mean for all samples falls below the threshold % will be excluded)
Option 3:
Filter by Median
(Analytes whose median for all samples falls below the threshold % will be excluded)
Option 4:
Filter by Sample threshold
At least one of the 2 selected groups
Both groups
must exceed the above threshold per analyte
In order for an analyte to be retained, the % of samples in one/both groups which are non-zero must exceed the threshold.
Option 5:
Remove all analytes containing null values
Sample Normalization Parameters
Normalize samples by:
None
Sample means
Sample sums
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