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pseudocount of dataset

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
• 2,584 views • link
written by yueli7 yueli7

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.

• 0 views • link
written by Mark Mark

Agreed. Please never use Excel for RNA-seq as it irreproducibly alters gene names and might converts numbers into letters, dates or something like that. Use established packages for RNA-seq, such as DESeq2 or edgeR or at least work in R or python rather than Excel.

• 0 views • link
written by ATpoint ATpoint

Agreed. Use those packages for bulk RNAseq data they are good and well tested.

• 0 views • link
written by Mark Mark

Hello, Amar,

Thank you so much for your great help!

Thank you again!

Best,

Yue

• 0 views • link
written by yueli7 yueli7

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

• 0 views • link
written by yueli7 yueli7

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