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Old 05-31-2014, 06:31 AM   #1
Location: Spain

Join Date: Nov 2013
Posts: 28
Default Getting normalized counts


I've tried to find differential expression with edgeR and DESeq2. These packages normalize my count data first, but they do not automatically provide normalized read counts to the end user. Any ideas how to obtain them through a series of R commands? Where could I look for this?

Thank you in advance!
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Old 05-31-2014, 08:30 AM   #2
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Location: Montreal

Join Date: May 2013
Posts: 367

For DESeq2, use the counts function, passing as arguments the DESeqDataSet object created by your call to the function DESeq, and the argument, normalized=True.

The function will return an integer matrix.
In the following example, I convert the matrix to a data frame.

# Create a DESeqDataSet object, and perform calculattions.
dds <- DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory="../../htseqcount", design= ~ condition)
dds <- DESeq(dds)

# Calculate and save the annotated normalized counts.
normalized.counts <- dds, normalized=TRUE ))
As to where you can get this information, you should read the DESeq2 vignette.
It is quite complete, and updated regularly.
After reading it a dozen times , I have a clearer idea how to use DESeq2, especially for more complex analyses, like multi-factorial analyses.

Last edited by blancha; 05-31-2014 at 08:38 AM.
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Old 05-31-2014, 09:20 AM   #3
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

For the edgeR verions, just:
normalized.counts <- 1e6 * cpm(dge)
where "dge" is a DGEList.
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