Hello,

I have a protein matrix, and want to use the justvsn function to normalize it.

After normalization, I found all the data are negative, the downstream function only works on positive value.

How can I change the parameter of vsn , them the output can be positive value?

Thank you in advance for great help!

Best,

Yue

Dear Yue,

I'm assuming that your data come in arbitrary units, i.e., are not measured in kilograms, moles or similar. The vsn transformation is, in the limit of large values (much larger than the inferred level of background noise), the same as a logarithm transformation, and I'm sure you're familiar with the relation $$ \log( ax ) = \log(x) + \log(a). $$ So you can always "lift" the result of calling vsn on your data $x$ into the range of positive values by multiplying them with some arbitrary, large enough, constant factor $a$ before calling vsn, or by adding a large positive constant afterwards. However, I'm worried that your downstream function is not applicable to these data, since such arbitrary choices (multiplying all values by the same constant) should not impact the result, if the result is to be meaningful. You may have to invest more thought or get consultation on a physically & statistically adequate choice of tool chain.

Wolfgang