Question: Z-Score On Raw Counts
0
gravatar for camelbbs
6.0 years ago by
camelbbs650
China
camelbbs650 wrote:

Hi All,

I have a question on normalization of rnaseq data. After I get raw reads counts from htseq-count, I want to use zscore to normalize it. Is that reasonable?

And how I can do that. If there have some guides, that will be very helpful.

Thanks a lot!

che

rnaseq • 3.6k views
ADD COMMENTlink written 6.0 years ago by camelbbs650

Can you specify why you want to z-transform the data? What are you planning to do with it? My first guess is that this is not a reasonable thing to do, but please provide more information all the same.

ADD REPLYlink written 6.0 years ago by Steve Lianoglou5.0k

I want to make heatmap. And Zscore can make the values centralized by 0, right?

ADD REPLYlink written 6.0 years ago by camelbbs650
2

You need to normalize your raw count data first. Z-score will standardize your data, but it won't normalize by library size. Another option is to use variant stabilization method provided by DESeq.

ADD REPLYlink written 6.0 years ago by Damian Kao15k
1

What Damian suggests is what you want....

ADD REPLYlink written 6.0 years ago by Sean Davis25k

Hi Damian, Thanks very much. DO you mean Zscore is not a normalization method? IS there any common method for normalizing the raw count, except for DESeq... Can I calculate RPKM first and then do zscore for rpkm...

ADD REPLYlink modified 6.0 years ago • written 6.0 years ago by camelbbs650

I also want to ask how to use zscore to standardize my data, is there any package in R?

ADD REPLYlink written 6.0 years ago by camelbbs650
1

Standardization can be done using the sweep() function in R.

ADD REPLYlink written 6.0 years ago by Sean Davis25k

Thanks a lot Sean.

ADD REPLYlink written 6.0 years ago by camelbbs650
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