Question

seeking a paper or journal review about repeated multiple testing for Biological ChIP-seq replicates?

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Jurat Shahidin ▴ 80

@jurat-shahidin-9488

Last seen 4.7 years ago

Chicago, IL, USA

Dear all:

I need to understand multiple repeated testing for biological ChIP-seq replicates, to observe test variation in repeated multiple test. Can anyone tell me any related papers, journal review to explain the topic that I raised? I also prefer to look at any existing Bioconductor packages that implement multiple repeated testing for ChIP-seq replicates. Thanks a lot.

Best regards:

Jurat

bioinformatics paper multiple treatments biologicalreplicates • 1.4k views

ADD COMMENT • link updated 8.4 years ago by Gordon Smyth 52k • written 8.4 years ago by Jurat Shahidin ▴ 80

score 4 · Accepted Answer · 2016-07-14

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Gordon Smyth 52k

@gordon-smyth

Last seen 4 hours ago

WEHI, Melbourne, Australia

As far as I know, there is no statistical method called "repeated multiple testing" or "multiple repeated testing".

If you simply mean "multiple testing", then you might look at the csaw package:

The csaw package is able to handle biological replicates and multiple experimental factors.

ADD COMMENT • link 8.4 years ago Gordon Smyth 52k

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Dear Gordon Smyth:

Thanks a lot for your quick respond here. I definitely look at that packages.

I aware that there is a case that repeating ChIP-seq replicates in several times, where each test would yield corresponding different experiment results, so I want to understand behind ideas of repeating test, and try to figure out test variation of one to another.Thank you

Best regards:

Jurat

ADD REPLY • link 8.4 years ago Jurat Shahidin ▴ 80