Hello,
When I upload my excel csv file does it matter if I upload normalized Log2(FC) values instead of concentrations. I only ask because I want to make sure my volcano plot and ANOVA are generated correctly and showing accurate representation of my data.
Thank you
Uploading a table of logFC values is not compatible with ExpressAnalyst.
You can upload normalized expression values (like log-CPM for RNA-seq or quantile normalized microarray, for example), and then select “None” during the normalization step. This allows you to use whatever method outside of ExpressAnalyst for filtering/normalization.
However, if you upload logFC values, differential expression analysis doesn’t make sense. These values are already compared to something (FC = group A/group B), so what is your comparison going to be for differential analysis? Any fold changes reported by ExpressAnalyst will be the ratio of two fold-changes that you uploaded, which doesn’t make any sense.
It’s possible to upload a list of genes with fold change values from a differential expression analysis that you performed separately, but neither ANOVA nor volcano plot tools exist for list upload (not compatible with the data format).