DispEsts plot
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Sep • 0
@06de5a1f
Last seen 8 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

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DESeq2 • 732 views
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@mikelove
Last seen 3 days 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.

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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:

enter image description here 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.

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

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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.

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Are the pairs nested within batch or across?

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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.

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