Thanks for the answer. is this mean that the gene is differentially more expressed in the population d compared to other populations? even though looking to the log2 mean expression that shows clearly the gene expression is more in z population! I get confused which graph to consider and why this differences!
both log2 and log2fc giving a completely huge difference of a gene in subpopulations
Hello, I am very new in the field of bioinformatics and data analysis, and I have a basic question and I would appreciate your help. Why find differences in the value of a specific gene in some subpopulations using the log2 mean expression distribution and log2FC differential expression output, both log2 and log2fc giving a completely huge difference? this gene is expressed in a specific population x using the log2 mean, and by using the log2fc, it shows in another population more compared to the log2! is that make sense?
1 answer
Because in loupe the logFC is not computed with respect to the same set of cells: it is always X vs not X. What that means is, if (in this case) population a and population d express a gene, and all other populations do not (or do not express it well), and d is much larger than a, then mean(d) - mean(not d) is much larger than mean(a) - mean(not a). And if z is a small number of cells, then mean(z) - mean(not z) will be the smallest, as not z contains both a and d.
I suspect that's what's happening here.
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Please add any data, plots or anything to illustrate the problem.
![enter image description here][1]
Yes. asking why expression levels and fold changes are different. I did t expect this difference, and which one to consider? for info the other genes didn't have this issue of this huge difference just some genes.. thanks