DESeq2 - groups with biological replicates from the same patient
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@399a8e69
Last seen 22 days ago
Spain

Hello, I have the following dataset.

Sample  Patient  Condition
Sample1 Patient1 Condition1
Sample2 Patient1 Condition1
Sample3 Patient2 Condition1
Sample4 Patient2 Condition1
Sample5 Patient3 Condition2
Sample6 Patient3 Condition2
Sample7 Patient4 Condition2
Sample8 Patient4 Condition2

Samples from the same patient are biological replicates since they were taken from the same culture in different days and processed separately. Should I add Patient in the design formula ~Patient + Condition or would it be fine if I leave ~Condition?

Thanks in advance.

Best regards,

S.

DESeq2 • 172 views
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@kevin
Last seen 1 hour ago
Republic of Ireland

I see no major issue using just ~ condition. Would we ever expect a situation whereby, e.g., Patient1 had both Condition1 and Condition2 (?) - rhetorical question.

If you proceed with just ~ condition, please check the PCA bi-plots to assess sample grouping.

they were taken from the same culture in different days

Keep in mind, therefore, that time may have an effect.

Kevin

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Hello. Thanks very much for your reply. The same patient won't be in both groups (the experiment does not have paired samples). I just have biological replicates from the same patient within the same group. These biological replicates should be almost identical but they were collected in different days and as you say time might have an effect. Thanks

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