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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Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM -
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...03-22-2024, 06:39 AM
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