normalizing three independent RNAseq samples

Question

[kanwarjag]

I have three RNAseq sample's read count and want to normalize the data with in each sample. What are my options. I was thinking of scaling data on the set of genes whose expression has not changed in all three samples. Any suggetsion?

Thanks

[ATpoint]

I was thinking of scaling data on the set of genes whose expression has not changed in all three samples

Good idea. Check the normalization methods in edgeR or DESeq2 which essentially do this. Are these samples from the same batch or lab or are they completely unrelated and therefore most likely confounded?

[kanwarjag]

Three independent samples from same lab differentiated to a particular same phenotype

[ATpoint]

In that case, you can use, as mentioned, the TMM method from edgeR or the geomatric mean approach from DESeq2. For simplicity, you can also run vst or rlog from DESeq2 which do normalization and log-transformation. All of the mentioned approaches are well-documented, please refer to the tool manuals and papers.