Entering edit mode

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.

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DispEsts plot

0

Entering edit mode

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.

```

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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:

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.

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

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.

Are the pairs nested within batch or across?

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

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.