filter data by normalization

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5.0 years ago

leandrogarcia20504 • 0

Hi everyone, I'm working with data from TCGA RNAseq with EdgeR.

My question is: "Can a filter my data according to normalization factors of each sample?"

For example, a have the samples:

Sample; libsize; norm.factors

 "TCGA.A7.A13G";   3771.01720124523;   0.794558677465975

"TCGA.AC.A23H";    4492.7373378347;     0.960628380498392

"TCGA.AC.A2FB";    4089.87064567962;    0.955022002308941

"TCGA.AC.A2FF";     4442.86994161128;    1.03356026473406

Could I exclude samples that have a greater deviation of 1?

Can I do this, to avoid large deviation of expression values?

Thanks for your attention!

RNA-Seq R edgeR tcga • 831 views

ADD COMMENT • link updated 4.9 years ago by Biostar 20 • written 5.0 years ago by leandrogarcia20504 • 0

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Hey Leandro, what is the range of the norm.factors?; what is your ultimate goal? Usually, EdgeR will automate the normalisation process, and estimate dispersion for you, too. Which commands have you run so far?

Perhaps this previous answer will help? - A: After Getting Normalization Factor Via Edger, What To Do For Normalization?

ADD REPLY • link 5.0 years ago by Kevin Blighe 87k

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