bumphunter output clarification
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chelsey.ju • 0
@chelseyju-12100
Last seen 3.7 years ago

Hello, 

I am looking for clarification and explanations for the following output headers of bumphunter DMR analysis:

 

        area cluster indexStart indexEnd L cluster p,value   p,valueArea  

 

Additionally, if a B=1000 permutation cut off was used, do the p values need to be further adjusted for multiple testing analysis or are they already corrected? 

 

thanks!

bumphunter DMR DMR analysis minfi bioconductor • 1.8k views
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rafa • 60
@rafa-7160
Last seen 2.2 years ago
United States

I would start by reading the Details section of the bumphunter help file. 

Regarding the table, each row is a candidate DMR.

value - is the average of the estimated coefficient (usually representing the difference between two groups) in the region

area - is the absolute value of the sum of the estimated coefficients in the region

cluster - the genome is divided into smaller regions, called clusters. We search for regions in each cluster to avoid going over a long stretch of the genome with no data. The value provided here is the ID for the cluster.

indexStart - is the index of the probe in the original methylation matrix where the region starts

indexEnd- is the index of the probe in the original methylation matrix where the region ends

L - is the number of probes in the region

clusterL - number of probes in the cluster

p.value - are explained in the help file. These do need multiple comparison corrections.

fwer - are explained in the help file. These do not need multiple comparison corrections

 

 

 

 

 

 

 

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This is helpful! Can anyone clarify what the difference is between the region and the cluster on this bit?:

L - is the number of probes in the region

clusterL - number of probes in the cluster

 

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A cluster is defined purely based on the array design (the spacing between probes). It is a collection of probes where the between probe distance (on the genome) is smaller than X. If X is set to be Inf, each chromosome will be a cluster. A region is (always) a subset of a cluster and is a set of probes which are differentially methylated. So that depends heavily on the actual observed data. Best, Kasper On Fri, Jan 6, 2017 at 3:12 AM, brhead [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User brhead <https: support.bioconductor.org="" u="" 11927=""/> wrote Comment: > bumphunter output clarification > <https: support.bioconductor.org="" p="" 90751="" #90845="">: > > This is helpful! Can anyone clarify what the difference is between the > region and the cluster on this bit?: > > L - is the number of probes in the region > > clusterL - number of probes in the cluster > > > > ------------------------------ > > Post tags: bumphunter, DMR, DMR analysis, minfi, bioconductor > > You may reply via email or visit https://support.bioconductor. > org/p/90751/#90845 >
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That clears it up! Thank you!

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