I downloaded the R package MetStat to preform an ASCA. I’m currently working through how best to organize the data because you input two dataframes. This is the example I’m working with.
I believe the first dataframe or the ‘data’ will only contain a list of the proteins and abundances (“variables are represented by columns, observations by rows”). Proteins will be in rows columns and abundances will be in columns rows– however, I don’t think order will be considered. Unless proteins should be in columns with abundance in rows… I’m going to look more into this tomorrow or Thursday since the ASCA is supposed to take into consideration time (that was the whole point) and I’ll update this. because observations are measured values (eg. abundance) and variables are what is observed/measured (eg. proteins).
The second dataframe or ‘levels’ will contain the temperature data for each protein/observation (“numeric matrix describing the experimental design. Each factor is represented by a column. The elements of the columns give the treatment level the row belongs to”). There will be one column representing a signal factor (temperature) and the elements will be 23 or 29, but I’m not sure how/if I can make time a factor?
I think the column would have to be “3, 5, 7, 9, 11, 13, 15” repeating, and I need to make sure that the order of proteins is the same for both dataframes so that the elements (23 or 29C) correctly match the factor (temperature). The data will only be described by temperature.
This will be okay since I will only use Silo 3 and 9. If I decide to do an ASCA between the 23C silos then I will make the elements “silo 2” or “silo 3″ for the factor.
Equation elements are specified as a string that indicates the factor to use in the ASCA. Factors are specified by the column (eg. =”1″) or interacting factors can be considered (=”123″). Multiple factors can also be entered (=”1,2,12”).
ASCA.Calculate(data, levels, equation.elements ="")
I wrote up an issue for help in our github.