Hi All,

The following code chunks, that is used to filter out genes less than 10 counts did not work at all because genes with less than 10 is still in the count matrix after running those commands. Anyone has any suggestion or could spot what was wrong there

> ## Create DESeq2 object ============================================
> 
> dds <- DESeqDataSetFromMatrix(countData = Raw.Count,
>                                   colData = Phenotype,
>                                   design = ~ Group)
> 
> 
> ## Estimate size factor ===========
> 
> dds <- estimateSizeFactors(dds)
> 
> ## Prefiltering: not necessary for DESeq, but good to reduce memory size and incrase speed of transformation =========
> 
> keep <- rowSums(counts(dds)) >= 10
> 
> dds <- dds[keep,]
> 
> ## print size factor ===========
> 
> sizeFactors(dds)
> 
> ## Normalized count 
> 
> normalized_counts <- counts(dds, normalized=TRUE)
> 
> dim(normalized_counts)
> 
> ## Write the csv file ==================
> 
> write.csv(normalized_counts, file="normalized_count.csv")

Thanks,

Synat