There are packages designed for this, e.g. SVA.
I will include batch as a covariate in the statistical model.
Take a look at this thread: http://seqanswers.com/forums/showthread.php?t=44083
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clinical RNA-Seq: batch effect
Hi all,
I have RNA-Seq data set coming from a clinical trial. The samples were extracted and sequenced at different days. That is, each individual sample could be processed separately. When a sample is available, it could be put together with other samples in other projects and run on the sequencer.
Do you have an idea how to effectively remove the batch effect?
Any advice will be appreciated.
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...07-08-2024, 03:19 PM
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