pseudocount of dataset

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4.5 years ago

yueli7 ▴ 250

Hello,

I have a RNA-seq data set.

How I can adding a small pseudocount to the entire dataset?

What is the pseudocount mean?

For example: 3.14159265, if I used excel function round(3.14159265,2)=3.14?

My understand is correct?

Thanks in advance for great help!

Best,

Yue

RNA-Seq • 2.0k views

ADD COMMENT • link 4.5 years ago by yueli7 ▴ 250

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That's not what pseudocount means (rounding a number is not pseudocount) and you shouldn't just randomly add a small number to the entire dataset. My guess is you want to somehow work with 0 values. I think this Reddit thread gives a a good definition of pseudocounts: https://www.reddit.com/r/bioinformatics/comments/8acfss/can_someone_give_a_pseudocounts_for_dummies/

You should use RNAseq packages that will handle pseudocounts for you appropriately.

ADD REPLY • link 4.5 years ago by Mark ★ 1.5k

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Hello, Amar,

Thank you so much for your great help!

Thank you again!

Best,

Yue

ADD REPLY • link 4.5 years ago by yueli7 ▴ 250

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Just add 0.8 in each number (column or row). 0.8 is a pseudocount, just not let any number to be 0.

ADD REPLY • link 4.5 years ago by yueli7 ▴ 250

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