User: alfonsosaera

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Posts by alfonsosaera

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bumphunter for 3 (or more) groups
... Dear BioStar Users, I am using [minfi][1] to analyze the results of an EPIC array. To check differential methylation I decided to look for differentially methylated regions (DMRs) using [bumphunter][2] as [recommended][3]. `bumphunter` function returns candidate DMRs with several columns of infor ...
bumphunter methylation epic array minfi dmr written 3 months ago by alfonsosaera0
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Comment: C: methylation array group probes
... In relation to this question, @Charles Warden, how would you compare DMRs among 3 different conditions? I understand bumphunter output for 2 groups but I do not see the logic for 3 groups. Thank you! EDIT: I opened a new [post][1] describing my doubts more deeply. [1]: https://www.biostars.org/p/ ...
written 3 months ago by alfonsosaera0
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Comment: C: Tools For Metagenomic Data Analysis
... Great tool! I really recommend it. ...
written 3 months ago by alfonsosaera0
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Comment: C: samr vs limma packages. How do you decide between them?
... Thanks for your answer! I think I will stay with limma, it is more or less accepted as the standard and it provides p-values and q-values (FDR) that fit most of my needs. ...
written 5 months ago by alfonsosaera0
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Comment: C: samr vs limma packages. How do you decide between them?
... Thanks again! the paper is very interesting. From the paper it appears that Limma and SAM work very similar when DEGs differ hihgly from the non-DEGs in the dataset. When the DEGs are closer to the non-DEGs Limma performs slightly better. ...
written 5 months ago by alfonsosaera0
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Comment: C: samr vs limma packages. How do you decide between them?
... Thanks for your comment @b.nota, I started with Limma because it is the accepted standard for microarrays but then heard about samr and I could not find any benchmark or comparison of the 2 methods. ...
written 5 months ago by alfonsosaera0
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samr vs limma packages. How do you decide between them?
... Dear BioStar Users, I am new in the BioStar community, I tried to search for posts that answer my question but I couldn't find any. Please forgive me if this has been already answered. I need to analyze a microarray dataset so I decided to use the bioconductor package I knew for this task, [limma ...
array R written 5 months ago by alfonsosaera0 • updated 5 months ago by Charles Warden7.0k

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