how to analysis technical replicates data?
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6.3 years ago
Yizhao ▴ 10

Hi all,

I've got protein MS data that contains 3 technical replicates. For all I know, technical replicates can examine the repeatability of technology. So, I will focus on those overlapped proteins between all 3 replicates. After that, I want to conduct differential expression analysis. Here comes the question. How do I do with the data from 3 replicates? Average 3 protein density values of 3 replicates as the protein's density? Is that OK? OR some other good ideas?

Any advice will be appreciated.

THX in advance.

best,

Yizhao

 

biostatistics statistics • 3.4k views
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6.3 years ago
Asaf 8.6k

I think you should take the sum of all technical replicates.

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Thx, and now, I have the same idea with you.

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6.3 years ago
Woa ★ 2.8k

You can use technical replicates to measure the variance(equivalent to noise ) of your data, and above the observed variance, you consider everything as signal. Often fold-change cut-off to ascertain differential expression is determined this way:

See this paper and related papers from the same group:
http://www.hindawi.com/journals/jdr/2012/168602/ 

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But then you won't take into account biological noise.

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Yes, I can do nothing to avoid the bias caused by sampling, or biological noise. But, actually, my experimental samples were sampling through  a time line. At present, I have no idea about the analysis with time series data. Is there  a practical strategies, except that comparing pairwise time-point by fold-change?

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Yes. Fold-change cutoff was my choice in RNA-seq analysis. Thx a lot. Yizhao.

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