dot plot downloaded gst files - percent/cluster group study
In the dot plot section, what does percent and cluster--group--study mean? When saving each file what does the values represent? Are both of these files used to generate the dot plot? Is there a way to use these files outside of this program to generate my own figures?
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Official comment
Because dot plots represent two axes of information for each dot - scaled mean expression and the percentage of cells expressing for that gene and annotation - when you export to a flat GCT file you have to select which data series you want to use. The "cluster--group--study" is an SCP-specific way of referring to the current annotation that you are viewing, where "cluster" is the name of the annotation, "group" is the type (meaning categorical labels, as opposed to continuous numeric values), and "study" refers to the scope of the annotation, meaning it is valid for all clustering in that SCP study.
By using this series, you will be exporting the scaled mean expression values for the genes you entered. If you select "percent", then the values exported are not the expression values, but the percentage of cells for that gene/annotation combo that showed non-zero expression values.
The resulting GCT file is a flat expression matrix with additional header information. More information on this format is available here. Many bioinformatics tools do support using GCT files natively, though you can also remove the first two lines of the file and save it as a flat TSV matrix to use in almost anything.
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