Geuvadis Normalization method

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4.1 years ago

khatami.mahshid ▴ 30

Hi I am using the GEUVADIS dataset, in the readme of the project I found this paragraph talking about normalization:

Normalization: None: raw read counts
Library depth: Read counts scaled by total number of mapped reads (mRNA), or total number reads mapping to miRNAs (miRNA) per sample, then adjusted to the median of the sample set (45M for mRNA, 1.2M for miRNA)
Library depth and transcript length: RPKM
Library depth & expressed & PEER: Library depth scaling as above, removal of units with 0 counts in >50% samples, and removal of technical variation by PEER normalization

I can't understand the way they normalized data. can anybody help me, please?

thank you

snp RNA-Seq rna-seq • 770 views

ADD COMMENT • link 4.1 years ago by khatami.mahshid ▴ 30

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Isn't the first line saying no normalization?

ADD REPLY • link 4.1 years ago by GenoMax 147k

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I'm not sure , are you sure about this?

ADD REPLY • link 4.1 years ago by khatami.mahshid ▴ 30

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