Question

MethylPipe pvalue output

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746458071 • 0

@746458071-10583

Last seen 7.2 years ago

I'm using BSprepare function in R package MethylPipe to perform binomial test. The paper says "The resulting multiple-testing corrected p-values are stored on the disk in the Tabix compressed and indexed file, and are available in methylPipe through the BSdata class. "

I wonder how to get the original pvalue of binomial test (not multiple-testing corrected).

Thank you so much.

MethylPipe • 1.0k views

ADD COMMENT • link updated 8.0 years ago by kamal.fartiyal84 ▴ 10 • written 8.0 years ago by 746458071 • 0

score 0 · Answer 1 · 2016-05-03

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kamal.fartiyal84 ▴ 10

@kamalfartiyal84-7976

Last seen 5.3 years ago

Cancer Research UK Cambridge Institute

Hi,

Its not possible to get the original p-value at present as they are corrected for multiple-testing as soon as they are generated and this process is not optional in the present implementation of the software. To get the original p-values, the BSprepare function code need to be modified.

Thanks.

Kamal

ADD COMMENT • link 8.0 years ago kamal.fartiyal84 ▴ 10

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Hi Kamal,

Thank you for your answers.

I want to get the original p-values because the input data is so big (about 20G) that I split it to speed up. When I combined the result of every part , the output corrected p-values is not right. Do you have any other suggestions for me or is there a paramete for BSprepare() to speed up?

Thanks.

ADD REPLY • link 8.0 years ago 746458071 • 0