I am working with large RNA-Seq dataset downloaded from the NCBI GEO. I would like to export the normalized counts data from
DeSeq2 based on
size factor normalization for further downstream analysis. It seems like running
dds <- DESeq(dds) and
dds <- estimateSizeFactors(dds) outputs the same results. Is my understanding correct? Please let me know if I could use any of these to export the normalozed counts data.
library("DESeq2") dds <- DESeqDataSetFromMatrix(countData = round(Counts_data), colData = sample_info, design = ~ Disease_state) ## 1 dds <- estimateSizeFactors(dds) sizeFactors(dds) normalized_counts <- counts(dds, normalized=TRUE) write.csv(normalized_counts, file="normalized_counts.csv") ## 2 dds <- DESeq(dds) sizeFactors(dds) normalized_counts_DESeq <- counts(dds, normalized=TRUE) write.csv(normalized_counts_DESeq, file="normalized_counts_DESeq.csv")
Created on 2021-09-20 by the [reprex package](https://reprex.tidyverse.org) (v2.0.1)