NA values showing at duplicacy removal step

Question

[prithvi.mastermind]

While doing averaging for gene expression values, I'm getting NA values in the expression matrix. How to solve the error.

Load packages

library(affy)
library(limma)
library(oligo)
library(pd.mogene.2.0.st)
library(genefilter)
library(arrayQualityMetrics)
library(mogene20sttranscriptcluster.db)
library(AnnotationDbi)
library(tidyverse)
library(factoextra)
library(ggplot2)
library(ggrepel)
library(NOISeq)
library(annotate)
library(NOISeq)
library(sva)
library(Biobase)
library(oligo)
library(biomaRt)
library(hugene20sttranscriptcluster.db)
library(dplyr)

celfiles <- list.files(pattern = "\\.CEL$", full.names = TRUE)
rawData <- read.celfiles(celfiles)

nromaliizing the data

normdata <- rma(rawData)

fetching expression data of normalized data as a data frame

normalized.exprs<-as.data.frame(exprs(normdata))

annotation_data <- data.frame(Sample = colnames(normalized.exprs))

types <- c(rep("IL", times = 4),
  rep("NIL", times = 4),
  rep("control", times = 4),
  rep("hypoxia", times = 4),
  rep("normoxia", times = 4))
annotation_data <- cbind(annotation_data, types)

DO BATCH CORRECTION

DATA_BC<- readData(normalized.exprs, factors = annotation_data)
myPCA = ARSyNseq(DATA_BC, factor = "types", batch = FALSE, norm = "n", logtransf = TRUE)
DATA_BC_DONE <- assayData(myPCA)$exprs

z-score transformation

transposed_matrix <- t(DATA_BC_DONE)
z_tr_mt <- scale(transposed_matrix, scale = TRUE, center = TRUE)
z_score <- t(z_tr_mt)

map probe ids to gene symbols and duplicate gene removal

probeids <- row.names(z_score)
gene.symbols <- mapIds(mogene20sttranscriptcluster.db, keys=probeids, column="SYMBOL", keytype="PROBEID")

normexprs = cbind(gene.symbols,z_score)
countmat = na.omit(normexprs)

double_matrix <- data.frame(countmat)

AGG <- aggregate(double_matrix[,-c(1)], by=list(Gene = double_matrix$gene.symbols), FUN=mean, na.rm =TRUE)
   rownames(AGG) <- AGG[,1]
   AGG[,1] <- NULL

I'm getting the following values after aggregation as all expression values are NA