Dear Lukas,
looking at the logFC values in my toptable results, I am confused as to how diffcyt calculates logFC values. If I use the median values, either in my DA or DS results, to calculate log fold change by hand, I end up with completely different values to those in the toptables, even trying out base 2 and 10 for the logarithm or calculating it on untransformed and arcSinh(x/5)-transformed values.
Regards.
Luka
Dear Lukas,
looking at the logFC values in my toptable results, I am confused as to how diffcyt calculates logFC values. If I use the median values, either in my DA or DS results, to calculate log fold change by hand, I end up with completely different values to those in the toptables, even trying out base 2 and 10 for the logarithm or calculating it on untransformed and arcSinh(x/5)-transformed values.
Regards.
Luka