what is meaning of blue line and dot line in scatter plot generated by cummRbund?

Question

[hana]

Can anyone explain for me the meaning of blue line and dot line in scatter plot generated by cummRbund?

Thanks in advance

[Devon Ryan]

What plot are you talking about? We have no way of magically knowing. Are you talking about something that looks like this:

[hana]

Yes, exactly. And I would like to know what is blue line and dot line means?

Thank you

Answer 1

[Devon Ryan]

The dashed line is simply a line with slope 1 and intercept 0. In other words, if the two things you're comparing have a correlation coefficient of 1, the dots will cluster along that line. The blue line is a regression along the actual points that you have, so you can see how your actual correlation deviates from 1.

[Devon Ryan]

BTW, the purpose of diagnostic plots like this is to ensure that normalization went OK. We normally assume that most genes aren't differentially expressed, or if they are that you have approximately equivalent numbers up/down regulated between groups (if you can't assume this for a dataset, then you should not use cuffdiff). Consequently, any two samples should generally have a high correlation after normalization.

[hana]

Thank you :)