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[BioC] Lumi: filtering and batch effects (combat)

Simone de Jong
Feb 25, 2008 at 11:26 pm
Dear List,

Since your responses helped me many times before, I'm posting two more
questions about Lumi:

* Can I filter genes that are below a certain detection pvalue out of my
file to speed up following analyses? How can I do that, at what stage and
what should be the threshold?

* I'm suspecting a batch effect in my data. I can work with ComBat, but I've
no idea how to get the adjusted values back into Lumi (a lumibatch) to go on
with transformation and normalization procedures. Any ideas?

Thanks,
Simone


___________________
Simone de Jong, Msc.
PhD student
The Netherlands
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1 response

  • Pan Du at Feb 26, 2008 at 4:27 pm
    Hi Simone,

    You can find your answers from the lumi vignette (latest version is 1.5.17).

    For your first question, you can use detectionCall function to select the
    threshold of deteciton p-value cut-off (0.01 by default).
    For example:
    presentCount <- detectionCall(example.lumi, Th=0.01)
    selDataMatrix <- dataMatrix[presentCount > 0,]
    See the use case in the vignette for more details.

    For the inverse transformation of VST, there is a function inverseVST. Now
    it only works for the RSN or SSN normalization algorithms. Please see the
    vignette for more details.


    As for batch effects, it is always a problem for microarray analysis. That's
    why we strongly suggest doing the experiment in the same batch. Different
    normalization methods or modeling can help to reduce the batch effects
    somehow. But they are always based on some assumptions. These assumptions
    may not work for some cases.


    Pan



    On 2/26/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
    wrote:
    Message: 8
    Date: Tue, 26 Feb 2008 00:26:22 +0100
    From: "Simone de Jong" <s.d...@...nl>
    Subject: [BioC] Lumi: filtering and batch effects (combat)
    To: <bio...@...ch>
    Message-ID: <002a01c87805$d64fc220$56a32f0a at cog063>
    Content-Type: text/plain; charset="us-ascii"

    Dear List,

    Since your responses helped me many times before, I'm posting two more
    questions about Lumi:

    * Can I filter genes that are below a certain detection pvalue out of my
    file to speed up following analyses? How can I do that, at what stage and
    what should be the threshold?

    * I'm suspecting a batch effect in my data. I can work with ComBat, but I've
    no idea how to get the adjusted values back into Lumi (a lumibatch) to go on
    with transformation and normalization procedures. Any ideas?

    Thanks,
    Simone


    ___________________
    Simone de Jong, Msc.
    PhD student
    The Netherlands

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