Q1: I am creating multiple experiments with the same set of samples and each time I have to input the parameter values. Is there a way to save the parameter values and re-load it each time a new experiment is created?
To use the same parameter values for subsequent experiments please follow the steps below:
In the Experiment Grouping Window --> Save the parameters by clicking on 'Save experiment parameters to file' icon
In the new experiment --> Experiment Grouping --> Click on 'Load experiment parameters from file' icon to import it.
Q2. I would like to change the experiment grouping in the middle of the analysis. If I change the parameters would the analysis change?
Changing the parameter values in the experiment grouping window will not change the results of previous analysis.
The project hierarchy will separate the two analysis from each other.
The concept of 'Multiple Interpretation Creation' will help you to follow different analysis steps in the same experiment.
The interpretation will have the information about the parameters included or excluded in the experiment and based on the interpretation selected the analysis will be done.
Q3. Is there a way to import the parameters for the same (sub) set of samples - from another experiment (located in the same project)?
The parameters could be brought in from one experiment to the other by following the steps below:
1.In the 'Experiment grouping' window for Experiment 1 --> Select the 'Save Experiment parameters to file' icon (second icon) --> Save to the desired location.
2. In the 'Experiment grouping' window for Experiment 2 --> Select the 'Load Experiment parameters from file' icon (first icon)--> Select the parameter file saved from Experiment1 --> Parameters get imported into Experiment 2.
Q4. How do I obtain an entity list of the genes that are expressed, and to what extent, in only one cell type?
To see the gene expression in only one cell type, create an interpretation with the 'cell type' of interest and perform the further analysis.
Ex: Filter on expression, Statistical Analysis, Fold Change
