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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.

  • #2
    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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