I'm new in bioinformatic and I would like to normalize HTseqcount data to do a survival analysis. How can I choose the best normalization ?
I tried to use DESeq2 with the median ratio method and normTransform but all medians are not align ...
DESeq_object <- estimateSizeFactors(DESeq_object) counts_normalized <- counts(DESeq_object, normalized = TRUE) boxplot(log2(counts_normalized + 1), main = "Counts normalized + log2 transformation")
I tried this too :
DESeq_object <- DESeqDataSetFromMatrix(countData = count, colData = coldata, design= ~ gender) vst_object <- varianceStabilizingTransformation(DESeq_object) boxplot(assay(vst_object))
How can I align all medians to have a good normalization ?
Thank you for your help !!