This depends on the biological questions under investigation. Within the context of MetabAnalyst support. Here are three steps:
1. Using technical replicates for QC
If the purpose of technical replications is to see if there is systematic variance introduced by sample handling or instrumentation, the clustering programs such as PCA or hierarchical clustering (in the Statistics module) can be used to investigate whether the same technical replicates tend to group together.
2. Merging technical replicates for analysis
Technical replicates are not independent biological samples, and should not be used directly for statistical analysis, which will inflate the statistical power. After checking the clustering pattern of these technical replicates, a common practice is to merge all sample replications. Please download upload the data to MetaboAnalyst (under Other Utilities => Merging Technical Replicates). Users have the options to merge technical replicates based on
- Mean
- Median
- Sum
- Minimum
- Maximum
- 1st Quarter
- 3rd Quarter
3. Uploading to compatible modules
The merged dataset is now suitable for statistical analysis and functional analysis in MetaboAnalyst which generally assumes all samples are independent biological replicates.