Flat Volcano plot

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3.2 years ago

vin23 ▴ 10

Hello everyone I have performed differential expression analysis on human dataset (GPL14550 Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (Probe Name Version)). I have 12 samples of Th1 and Th2 sample type. At the end I visualized the top genes using volcano plot and it came out weird as shown in image. Please help me to figure it out.

Differential R Volcano Expression plot • 2.0k views

ADD COMMENT • link 3.2 years ago by vin23 ▴ 10

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It probably means that you have only adjusted p-values very close to 1, so no differential expression. What is the output of a summary() when you run it on the adjusted p-value column of the results?

ADD REPLY • link 3.2 years ago by ATpoint 85k

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This is the output of summary(tab$adj.P.Val)

Min. 0.994 1st Qu. 0.9994 Median 0.9994 Mean 0.9994 3rd Qu. 0.9994 Max. 0.9994

ADD REPLY • link 3.2 years ago by vin23 ▴ 10

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There you go, no differential genes. The study could be underpowered or there are no DEGs, or batch effects make dispersion large.