Hi Alexander,
I hope you are doing well.
My name is Emanuel, and I am a PhD student at Human Technopole in Milan. First of all, I would like to say that I really appreciate the tool and the work behind it. It has been extremely useful for my GeoMx analyses.
I am currently analysing 13 GeoMx slides and using the multi-slide model for background noise removal. My understanding was that the multi-slide model should also help mitigate potential batch effects arising from slide-to-slide differences.
However, after running the model, I can still observe a noticeable batch effect across slides. I was wondering whether my understanding is correct, or if additional normalisation or correction steps are typically required after using multi-slide model.
I was also wondering whether increasing the number of samples drawn from the posterior distribution could help reduce this issue, or if this is unlikely to address the observed batch effects.
Would you have any suggestions or recommendations on how to address this issue?
Thank you very much for your time and help.
Best regards,
Emanuel
Hi Alexander,
I hope you are doing well.
My name is Emanuel, and I am a PhD student at Human Technopole in Milan. First of all, I would like to say that I really appreciate the tool and the work behind it. It has been extremely useful for my GeoMx analyses.
I am currently analysing 13 GeoMx slides and using the multi-slide model for background noise removal. My understanding was that the multi-slide model should also help mitigate potential batch effects arising from slide-to-slide differences.
However, after running the model, I can still observe a noticeable batch effect across slides. I was wondering whether my understanding is correct, or if additional normalisation or correction steps are typically required after using multi-slide model.
I was also wondering whether increasing the number of samples drawn from the posterior distribution could help reduce this issue, or if this is unlikely to address the observed batch effects.
Would you have any suggestions or recommendations on how to address this issue?
Thank you very much for your time and help.
Best regards,
Emanuel