Question: Scaled gene expression data and produced negative value
0
gravatar for Nan
13 days ago by
Nan0
Nan0 wrote:

Hi, I have a data table of gene expression which contains TPM value. So here I try to do a heatmap plot. So I scale by gene level at first and produce negative value. So why negative values comes up?

rna-seq R gene • 134 views
ADD COMMENTlink modified 12 days ago • written 13 days ago by Nan0
3

What kind of scaling have you done?

If it's log scale or zscore there will be negative values for values less than 1

ADD REPLYlink modified 12 days ago • written 12 days ago by dare_devil1.3k

Can you include your code here?

ADD REPLYlink written 12 days ago by rpolicastro3.2k

rowScales(data) - Very simple code.

ADD REPLYlink written 12 days ago by Nan0
1

That's not as simple as you claim - which package is rowScales from? Why are you using it instead of scale?

ADD REPLYlink written 12 days ago by _r_am32k
1

Why don't you share us the package name used in R? Tell us about the function rowScales

ADD REPLYlink modified 12 days ago • written 12 days ago by dare_devil1.3k
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