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wyang17 / SQuIRE

Software for Quantifying Interspersed Repeat Expression
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Batch Effect Correction in SQuIRE #63

Open fernandogs97 opened 2 years ago

fernandogs97 commented 2 years ago

I have been working with SQuIRE a few months performing different analysis with the samples of my laboratory. Now, I am going to start analyzing samples of different laboratories for increasing the number of samples and my statistical power. I have been reading about it and the developers of DESEQ2 (the part of SQuIRE that performs the differential expression analysis) recommend to introduce the batch variable so the algorithm can take into account the differences between samples produced by its origin. How can I introduce this variable if I am using SQuIRE? Is necessary to perform this after the mathematical correction performed by this sofware?

GiwaAO commented 2 years ago

I would think that you will have to introduce the batch variable in call_deseq2.py and call_deseq2_prefilter.py scripts. & probably also define inputs for batch in the call.py/cli.py script.. However, i think the easiest would be to output the count tables and run the DESeq2 analysis yourself accounting for the batch effects. My thoughts