## User: Ankit

Ankit •

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#### Posts by Ankit

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... I am still not clear which test to use. Please help. ...

written 6 days ago by
Ankit •

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... ![Here is the image attached]
https://ibb.co/g4BkhTY ...

written 7 days ago by
Ankit •

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... We have methylation EPIC array data 850K for five individals as I previously mentioned.
After normalization and filtering ~750K probes left. I would like to compare global or overall methylation profle for control vs patient. I would like to see if there is a significant difference between the two ...

written 7 days ago by
Ankit •

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... So my data has ~750,000 methylation array probes.
I first plotted the boxplot and then violin.
I have five individuals with varying methylation profile for each probes. So which test do you think is applicable to this kind of data, if I want to compare control with any of the 2 patient I have?
...

written 7 days ago by
Ankit •

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... Yes you are right.
So as #Carambakaracho suggested, I will apply t-test? ...

written 7 days ago by
Ankit •

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... Thanks for reply.
So I apply t-test for control vs patients? Is it Unpaired t-test?
Please help
Thanks ...

written 7 days ago by
Ankit •

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... Hi,
I have 5 samples (1 control +2 patients + 2 parents) for which I plotted an average methylation profile using violin plot. I would like to know which statistical test I need to apply to compare control vs patients 1/ patient2?
An example plot is like similar to this [google image][1]:
Thanks
...

written 7 days ago by
Ankit •

**100**• updated 7 days ago by Carambakaracho •**1.2k**0

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... Hi,
Thank you for the suggestion.
Using p.value provided by Deseq2, I recalculated padj (using p.adjust(p.val, method ="BH")).It matched with p.adj value provided by Deseq2.
But
Can I apply fisher.test function on raw/normalized count matrix to get p.value gene-wise?
Later I can apply the fun ...

written 7 days ago by
Ankit •

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... Thanks.
Fisher.test gives only one p-value for contingency table. How will I get gene-wise p-values (as show in the table above or as obtained from DESeq2 normalisation)? ...

written 10 days ago by
Ankit •

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... Thanks for the response.
This function will work on p-values as input.
*As in manual:*
**Given a set of p-values, returns p-values adjusted using one of several methods.**
I have DEseq2 normalized count matrix. How should I proceed in that case? ...

written 10 days ago by
Ankit •

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