Z-Score On Raw Counts

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11.5 years ago

camelbbs ▴ 710

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 • 7.3k views

ADD COMMENT • link 11.5 years ago by camelbbs ▴ 710

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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 REPLY • link 11.5 years ago by Steve Lianoglou 5.2k

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

ADD REPLY • link 11.5 years ago by camelbbs ▴ 710

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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 REPLY • link 11.5 years ago by Damian Kao 16k

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What Damian suggests is what you want....

ADD REPLY • link 11.5 years ago by Sean Davis 27k

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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 REPLY • link 11.5 years ago by camelbbs ▴ 710

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

ADD REPLY • link 11.5 years ago by camelbbs ▴ 710

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

ADD REPLY • link 11.5 years ago by Sean Davis 27k

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Thanks a lot Sean.

ADD REPLY • link 11.5 years ago by camelbbs ▴ 710

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