Can GSVA be applied in several sample type and each type only have two replicates ?
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@shangguandong1996-21805
Last seen 8 months ago
China

Hi,

In the GSVA article, it says that

The user should also be aware that the non-parametric density estimation within the GSVA algorithm requires a sufficient number of observations which, according to our analysis of statistical power in Figure 2, should be larger than n=10.

So it means that I should have enough sample n to get a non-parametric density estimation. I have read the GSVA manual, and find all the data have more than 10 samples in one conditon.

But I am wondering whether GSVA can be applied in my experiment. My experiment have 8 time point, and each time point have 2 replicates. The total n is 16 here, but I am wondering whether I can use GSVA in this 16 samples.

Best wishes

Guandong Shang

GSVA • 197 views
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Robert Castelo ★ 2.9k
@rcastelo
Last seen 4 days ago
Barcelona/Universitat Pompeu Fabra

Dear Guandong,

sorry for the very late reply to your post, I somehow overlooked it. The non-parametric density estimation is made using all available samples and therefore, the recommendation about having at least n=10 samples for the whole sample size, not per condition. So, having n=16 meets that minimum recommendation.

cheers,

robert.

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