RNA-seq Normalisation methods to compare using raw miRNA data
Hello members!! I have a raw data file of miRNA sequence data (Read counts file). I need suggestion for few normalisation methods that I could use to normalise the data. So far i have used (Size factor and logFC paramaters of) DESeq2 and (TMM of) EdgeR. I cannot use RPKM because the raw data file doesnt contain any read lengths. Kindly advice me what can be considered for the same Thank you
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raavi21198 •
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rlog or vst worked nicely for me but you have to check with your data what works best for you. Make and RLE plot and see the differences.
Sure. Thank you for your response!!