qq-plot not start from the 0
1
0
Entering edit mode
3.8 years ago
ubs717 • 0

Hi everyone, I did the GWAS analysis and got the result from TASSEL with GLM. Then I tried to make a qq-plot based on the p-value from GWAS output result. However, the qq-plot always started from y-axis 1 but not from 0 no matter how I modified the calculation. Following is the linkage for one of my qq-plot, please check it.

https://www.dropbox.com/s/7b1eo4flefb3q10/QQ_plot_Leaf_GWAS%20_%20miR396e-5p%20_%20length_specific_boxcox_transform_5genetic_2Latent.jpg?dl=0

Please, any suggestion?

Best, Shu-Yun Chen

qq-plot • 987 views
ADD COMMENT
0
Entering edit mode
3.8 years ago
theobroma22 ★ 1.2k

It makes sense to me - guessing from your plot it shows that your pvalues range from 0.15 to 1E-7, right? If so, -log of 0.15 = 0.82 and -log of 1E-7 = 7. If you thought it should start from 0 means you have pvalues equal 1, cause -log of 1 = 0. Do you have pvalues equal to 1??

ADD COMMENT

Login before adding your answer.

Traffic: 1550 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6