Using DESeq2 normalisation method on a tximport list of matrices without sample information
1
0
Entering edit mode
user31888 ▴ 30
@user31888-9209
Last seen 5.3 years ago
United States

 

From the DESeq2 vignette:

txi <- tximport(files, type="salmon", tx2gene=tx2gene)

ddsTxi <- DESeqDataSetFromTximport(countData = txi, colData = samples, design = ~ condition)

Q1. Is it possible to normalise a gene expression matrix (produced by Salmon and tximport) using DESeq2 method without sample information?

The goal here is to obtain a DESeq normalised expression matrix.

Q2. As an alternative, would it be coherent to normalise a matrix of raw read counts manually by the method of median of ratios (described here)?

Q3. Is it correct to say that RLE is the DESeq2 normalisation method, whereas the median of ratios was the previous DESeq method?

deseq2 • 1.3k views
ADD COMMENT
2
Entering edit mode
@wolfgang-huber-3550
Last seen 16 days ago
EMBL European Molecular Biology Laborat…

A1. Yes. Try giving a trivial dataframe for colData and a trivial design (like ~1) for design.

A2. I'd rather use the estimateSizeFactorsForMatrix for that alternative.

A3. No.
The normalization methods of DESeq2 and DESeq are (up to implementation details) the same.

ADD COMMENT
0
Entering edit mode

Thanks for your explanation !

ADD REPLY

Login before adding your answer.

Traffic: 806 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6