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al2na / methylKit

R package for DNA methylation analysis
https://bioconductor.org/packages/release/bioc/html/methylKit.html
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What does assocComp p-values suggest? #229

Closed geethavenk closed 1 year ago

geethavenk commented 3 years ago

Hi, I am analysing data from two batches and I would like to check if there are batch effects. The assocComp function returns association p-values (eg: $batch_id PC1 PC2 PC3 PC4 PC5
0.9635854342 0.0001077354 0.4936436113 0.0244559362 0.1797026503)

I am not sure if there is significant batch effects in this data. How can I decide which component should be used for remove Comp?

Thank you.

Best, GSK

al2na commented 3 years ago

PC2 seems to be associated with the batch, see if removing that helps with the clustering. You can also use the batch as a covariate during differential methylation calculation.

Best, altuna

On Mon, Jun 14, 2021 at 2:52 PM Geetha @.***> wrote:

Hi, I am analysing data from two batches and I would like to check if there are batch effects. The assocComp function returns association p-values (eg: $batch_id PC1 PC2 PC3 PC4 PC5 0.9635854342 0.0001077354 0.4936436113 0.0244559362 0.1797026503)

I am not sure if there is significant batch effects in this data. How can I decide which component should be used for remove Comp?

Thank you.

Best, GSK

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