R tutorials transformation

[mweberr]

Hi, I am just going through your R tutorials, which are very useful to learn phyloseq package.
One question I have is about the transformation of the read into relative data.

Why do you choose the median sum and not 100 or the minimum of all samples ?

total = median(sample_sums(carbom))
  standf = function(x, t=total) round(t * (x / sum(x)))
  carbom = transform_sample_counts(carbom, standf)

[vaulot]

Hi
Good question... In fact, the exact number you choose has no influence on the analysis. So you can choose any value you see fit: mean, median or minimum. Since you round, I would advise against 100 because then you would have rounding errors (in this case you would need to remove the round() function but this may cause problems with some downstream analysis that need integer values.