When I want to create an MA plot from the data normalized by rma method, the following error is shown. Could anybody help me solve this issue?

> library(affy)
> library(GEOquery)
> library(tidyverse)

> getGEOSuppFiles("GSE57178")
> untar("GSE57178/GSE57178_RAW.tar", exdir = "data/")
> data.affy <- ReadAffy(celfile.path = "data/")

> data.rma <- rma(data.affy)
> MAplot(data.rma, which = c(1:18), plot.method = "smoothScatter", type = "pm")
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function MAplot for signature "ExpressionSet"

> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8      
 [2] LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8      
 [8] LC_NAME=C                 
 [9] LC_ADDRESS=C              
[10] LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8
[12] LC_IDENTIFICATION=C       

tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets 
[6] methods   base     

other attached packages:
 [1] hugene10stv1cdf_2.18.0 lubridate_1.9.3       
 [3] forcats_1.0.0          stringr_1.5.1         
 [5] dplyr_1.1.4            purrr_1.0.2           
 [7] readr_2.1.5            tidyr_1.3.1           
 [9] tibble_3.2.1           ggplot2_3.5.0         
[11] tidyverse_2.0.0        GEOquery_2.70.0       
[13] affy_1.80.0            Biobase_2.62.0        
[15] BiocGenerics_0.48.1

The MAplot function from affy is meant for AffyBatch objects, not ExpressionSet, which is why you get the error. You can figure this out for yourself by checking the help page (which you seem to have done already - note that once you have summarized an AffyBatch, there are no longer any PM probes, so using type = "pm" should have been a hint). Alternatively, you can check the methods.

> showMethods(MAplot)
Function: MAplot (package affy)
object="AffyBatch"

Which indicates there is only dispatch on an AffyBatch.

You could do

MAplot(data.affy, plot.method = "smoothScatter", type = "pm")

To get MA plots for the PM probes. By definition this will use a pseudo-median as the comparator, and if that is what you are after (for the ExpressionSet), one alternative is in my affycoretools package.

library(affycoretools)
maplot(data.rma)