It's soo strange! :( This is the full code.

#######################Aphid Study###################################

# make class labels
class_Aphid <- c( rep("Mock_Aphid",3), rep("TuMV_Aphid",3) )


# Read in count matrix
rawdata_Aphid=read.table("gene_read_counts_table_Aphid_final.tsv.txt", header=TRUE, stringsAsFactors=FALSE, row.names=1)

# Check dimensions
dim(rawdata_Aphid)

# Require at least 1/6 of samples to have expressed count >= 10 #no need to run since its already ran above 
sample_cutoff <- (1/6)
count_cutoff <- 10

#Define a function to calculate the fraction of values expressed above the count cutoff  #no need to run since its already ran above
getFE <- function(data,count_cutoff){
  FE <- (sum(data >= count_cutoff)/length(data))
  return(FE)
}

#Apply the function to all genes, and filter out genes not meeting the sample cutoff
fraction_expressed <- apply(rawdata_Aphid, 1, getFE, count_cutoff)
keep_aphid <- which(fraction_expressed >= sample_cutoff)
rawdata_Aphid <- rawdata_Aphid[keep_aphid,]

# Check dimensions again to see effect of filtering
dim(rawdata_Aphid)

#Running edgerR #no need to run since its already ran above
library(edgeR)

###extracting groups from target file

y_Aphid <- DGEList(counts = rawdata_Aphid, group = class_Aphid)

head(y_Aphid)
nrow(y_Aphid)

#TMM normalization

y_Aphid <- calcNormFactors(y_Aphid)
y_Aphid$samples

# Estimate dispersion

y_Aphid <- estimateCommonDisp(y_Aphid, verbose=TRUE)
y_Aphid <- estimateTagwiseDisp(y_Aphid)

# Differential expressed genes test
et_Aphid <- exactTest(y_Aphid, pair = c("Mock_Aphid", "TuMV_Aphid"))

# Print top genes
topTags(et_Aphid)

# Print number of up/down significant genes at FDR = 0.05  significance level
summary(de_Aphid <- decideTestsDGE(et_Aphid, adjust.method="BH", p=.05))

out_Aphid <- topTags(et_Aphid, n="Inf", adjust.method = "BH", sort.by = "PValue", p.value = 0.05)
dim(out_Aphid)

write.table(out_Aphid, file = "TuMV_APhid_DE.txt", quote = FALSE, row.names = TRUE, sep = "\t")