Question: TCGA data and Sample size
gravatar for chowdhury
2.2 years ago by
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.


statistics tcga sample size • 944 views
ADD COMMENTlink modified 12 months ago by Kritika260 • written 2.2 years ago by chowdhury0
gravatar for Kritika
12 months ago by
Kritika260 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 12 months ago by Kritika260
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