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What does assocComp p-values suggest?
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
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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