Question: TCGA data and Sample size
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gravatar for chowdhury
20 months ago by
chowdhury0
chowdhury0 wrote:

Hi, I am new to statistics and bioinformatics. I have a very basic question regarding sample size. If I'm using TCGA data, and I select 600 lung cancer samples for expression analysis and along with it I select 60 adjacent control data (paired data). Will I get an error in the result (false positive)? Kindly explain.

Thanks

statistics tcga sample size • 764 views
ADD COMMENTlink modified 6 months ago by Kritika250 • written 20 months ago by chowdhury0
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gravatar for Kritika
6 months ago by
Kritika250
India
Kritika250 wrote:

Your 600 lung cancer samples are sequence data or microarray data? You can try generating PCA plot or heatmap with FPKM RPKM or count file (if this is sequenced data) After generating PCA plot you can select the group of sample take avarage and consider that as one and compare with your control. This will result less false positive. Also you can check abundance of the house keeping genes among 600 and control there should not be much variations

ADD COMMENTlink written 6 months ago by Kritika250
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