Hello everyone,

I have a count matrix which has 5 different tissue types. I did differential gene expression analysis to them as 2 samples each time (the analysis I need actually) but I am planning to generate heatmap, clustering analysis, PCA and SOM to all samples so I need normalized counts for each sample.

I used normTransform function to all data (designed as DESeq object but in the result list I could not find normalized values.

Is there any way to only have normalized values of a multi sample data without doing any analysis?

Thank you. 

To get counts that have been scaled to account for library size, you can do:

dds <- estimateSizeFactors(dds)
ncts <- counts(dds, normalized=TRUE)

If you just want the values that are in the DESeqTransform object, use assay(). See the transformations section of the vignette for more details on this.