Hello every body, I am trying to subset data in an gset, but I am running into issue. Here's essentially what I'm attempting:

library(Biobase) library(GEOquery) library(limma)

dataset <- "GSE21942" platform <- "GPL570"

load series and platform data from GEO

gset <- getGEO(dataset, GSEMatrix =TRUE, AnnotGPL=TRUE, destdir ="../data/" )

if (length(gset) > 1) idx <- grep(platform, attr(gset, "names")) else idx <- 1 gset <- gset[[idx]]

ex <- exprs(gset)

data normalization

ex <- log2(ex) ex <- normalizeQuantiles(ex)

sub-setting data

colnames(ex) <- c(paste("control", 1:15), paste("MS", 1:14)) ex <- ex[,!colnames(ex) %in% c("MS 10", "MS 11", "MS 13")] gr <- c(rep("control",15), rep("MS",11)) pData(gset) <- read.table("../source/phenod1.txt", header = T, sep="\t" )

exprs(gset) <- ex

After returning ex in to gset I encountered to this error: Error in .validate_assayDataElementReplace(obj, value) : object and replacement value have different dimensions

I know that now my assayData is different from my pData How can I solve the problem?