Question

DispEsts plot

0

Entering edit mode

Sep • 0

@06de5a1f

Last seen 14 months ago

Germany

Hi,

Given the following dispersion plots, is my data a good fit for the DESeq2 model? Thank you for your your kind help in advance.

enter image description here

```

DESeq2 • 921 views

ADD COMMENT • link 20 months ago Sep • 0

score 0 · Answer 1 · 2023-03-23

0

Entering edit mode

Michael Love 42k

@mikelove

Last seen 1 day ago

United States

You have a lot of high dispersion genes, check PCA plots, also count plots for the genes with high mean and high dispersion.

ADD COMMENT • link 20 months ago Michael Love 42k

0

Entering edit mode

Thanks a lot for your reply,

Based on your suggestion, I plotted the PCA and count plots (just for six of the variables)

The two plots are like the following:

enter image description here

Would you please help me if the DESeq2 would be useful otherwise do you have any other suggestion regarding the method for analyzing DEG?

Thanks a billion for your kind help in advance.

ADD REPLY • link 20 months ago Sep • 0

0

Entering edit mode

What are the sample size for the two groups? Have you included factors to account for unwanted variance?

ADD REPLY • link 20 months ago Michael Love 42k

0

Entering edit mode

The sample size is 50 for each group, (50 pre and 50 post), samples are paired. No. I have not included the factors to account for unwanted variance. If I want to do so the design formula would be ~ batch + subject + condition, given that samples are paired?

Thanks a billion for your kind help.

ADD REPLY • link 20 months ago Sep • 0

0

Entering edit mode

Are the pairs nested within batch or across?

ADD REPLY • link 20 months ago Michael Love 42k

0

Entering edit mode

I think it is across. My design matrix is like the following:

enter image description here

This is the only information I have regarding the samples. ( I mean I have only the samples measurements before and after the infection and nothing more like group, block, batch or so)

Thanks a lot for your kind help in advance.

ADD REPLY • link 20 months ago Sep • 0