How to analyze 10 samples (5 control, 5 treatment) which perform the experiment from different day
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Yosapol • 0
@40f341c9
Last seen 5 weeks ago
Netherlands

Dear all,

I have rna-seq data from 5 samples of control and 5 samples of treatment, total 10 samples. The experiment were performed in different day (one control and one treatment), in total 5 days.

What would be the best way to minimize batch effect? Would it be possible to test each pair of control and treatment independently?

Thank you very much for your suggestions. Best regards,


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
DESeq2 RNASeq • 166 views
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@mikelove
Last seen 3 days ago
United States

You can use ~batch + condition. See the vignette for more details.

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Thank you very much Michael Love , I followed the vignette and discussion on this forum. It is very useful. I have seen that when we put ~batch + condition in the design, it take into account on analysis, but not in PCA plot

Could you please suggest how to perform PCA when we take ~batch into account, without removing?

Best regards,

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See the FAQ.

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Thank you very much

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