Hi all!
I am trying to draw MA plots for my Affymetrix microarrays using affy package and function MAplot. I am trying to take a look at my raw data in AffyBatch object (1st microarray) as follows:
MAplot(data.raw, which=1)
However, I am keep on gettin an error stating:
Error in quantile.default(as.numeric(x), c(0.25, 0.75), na.rm = na.rm, :
missing values and NaN's not allowed if 'na.rm' is FALSE
I don't know how could I make it work? Any ideas and suggestions on what might be the issue will be appreciated.
Cheers! Agata
Thanks a lot Kevin!
However, if I understand correctly from the vignette you recommended, it should be possible to make an MA plot from AffyBatch object, including object with the raw data - the function should by default transform it to logarithms?
All the best, Agata
* EDIT *
I managed to plot M vs. A on the raw data by using only PM probes - otherwise there were missing values in my MM probes which were causing issues with MAplot() function: