affy MAplot NA error

Question

[ciemanek]

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

Answer 1

[Kevin Blighe]

Hi Agata,

You are not supposed to generate a MA plot from raw data. You first have to normalise your raw data and then pass the normalised object to MAplot().

Please take a look at the first few pages of the tutorial affyPLM: Advanced use of the MAplot function

Kevin

[ciemanek]

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:

MAplot(data.raw, which = 1, log = TRUE, type="pm")