Difference between numbers of perfect matches in oligo and affy packages.

Question

[Mohammad Ali]

Hi, I'm new at bioinformatics and I'm learning about "affy" and "oligo" packages by analyzing expression profiling data with accession number GSE99941. I ran pm() from "Affy" and "Oligo" but I got different outputs.

celpath <- "C:/Users/win/Desktop/Dataset/Dataset/"
li1 <- list.files(celpath , full.names = T)
library(oligo)
library(affy)
dat1 <- read.celfiles(li1)  #ExpressionFeatureSet
dat2 <- ReadAffy(celfile.path = celpath)
pms1 <- oligo::pm(dat1) #pm stands for perfect match.
pms2 <- affy::pm(dat2)

I also got a warning message when I ran dat2 <- ReadAffy(celfile.path = celpath):

Warning message:
The affy package can process data from the Gene ST 1.x series of arrays,
but you should consider using either the oligo or xps packages, which are
specifically designed for these arrays.

Is there a problem?