This is a test version of Biostars. For the public version, visit https://www.biostars.org.
DESeq without nornalization
I am working on a pre-processing method for differential expression analysis, and need to run DESeq method without normalization of input counts. I know that estimateSizeFactors function calculates the scaling factors and I guess estimateDispersions uses them. Is there anyway to bypass normalization in DESeq?
rna-seq
• 3,943 views • link
updated by Devon Ryan Devon Ryan • written by zamanys4 • zamanys4

1 answer

Just use the sizeFactors() accessor and set everything to 1.

• 0 views • link
written by Devon Ryan Devon Ryan

Hi,

What would be the command to avoid normalization if I have FPKM values in dataframe df. I am using following commands:

my_dds <- DESeqDataSetFromMatrix(countData = df, colData = my_Design, design = ~ condition)
my_res_LFC <- lfcShrink(DESeq(my_dds), coef = 2, type = "apeglm")
• 0 views • link
written by kashiff007 kashiff007

Log in to answer this question.

More posts like this