Question: How to do FDR p.adj manually on "mr.edgeR object" from MEDIPS package?
0
gravatar for pertille
3.1 years ago by
pertille0
Sweden
pertille0 wrote:

As I am working with a reduced-genome and the "p.adj" take in account all the  windows in the genome, this filter is eliminating all of my windows with differential methylation profile:

Using this command in MEDIPS package, I can do my differencial methylation analysis including de FDR correction and consequently without significant windows results:

mr.edgeR = MEDIPS.meth(MSet1 = MeDIP_AV, MSet2 = MeDIP_C, CSet = CS, p.adj = "fdr", diff.method = "edgeR", MeDIP = F, CNV = F, minRowSum = 10)

On the other hand, if I do this command without FDR filter, I get a fair number of significant windows at the level of 0.005% (~300 windows):

mr.edgeR = MEDIPS.meth(MSet1 = MeDIP_AV, MSet2 = MeDIP_C, CSet = CS, p.adj = "none", diff.method = "edgeR", MeDIP = F, CNV = F, minRowSum = 10)

Then I eliminate the windows that have no methylation coverage in the mr.edgeR (p.adj="none") using this:

mr.edgeR <- mr.edgeR[mr.edgerR$MSets2.counts.mean != c("0"), ]

 

and now I wanna do the manual FDR correction in "mr.edgeR" object

But I don´t know how. 

 

edger medips R • 536 views
ADD COMMENTlink modified 3.1 years ago by Lukas Chavez510 • written 3.1 years ago by pertille0
Answer: How to do FDR p.adj manually on "mr.edgeR object" from MEDIPS package?
0
gravatar for Lukas Chavez
3.1 years ago by
Lukas Chavez510
USA/La Jolla/UCSD
Lukas Chavez510 wrote:
Dear Pertille, indeed, testing a huge amount of genome wide windows causes strong effects by subsequent multiple testing. To avoid many potentially unnecessary tests, MEDIPS allows to set an arbitrary integer to the minRowSum parameter of the MEDIPS.meth() function. I am aware that any value for this parameter will be somewhat arbitrary. Reasonable values depend on your library and reference genome size (please apologise that I cannot give the best recommendation for this parameter). However, MEDIPS will then only consider genomic windows tested for differential coverage when applying multiple testing. All the best, Lukas On 10 Feb 2016, at 18:42, pertille [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User pertille<https: support.bioconductor.org="" u="" 9104=""/> wrote Question: How to do FDR p.adj manually on "mr.edgeR object" from MEDIPS package?<https: support.bioconductor.org="" p="" 78139=""/>: As I am working with a reduced-genome and the "p.adj" take in account all the windows in the genome, this filter is eliminating all of my windows with differential methylation profile: Using this command in MEDIPS package, I can do my differencial methylation analysis including de FDR correction and consequently without significant windows results: mr.edgeR = MEDIPS.meth(MSet1 = MeDIP_AV, MSet2 = MeDIP_C, CSet = CS, p.adj = "fdr", diff.method = "edgeR", MeDIP = F, CNV = F, minRowSum = 10) On the other hand, if I do this command without FDR filter, I get a fair number of significant windows at the level of 0.005% (~300 windows): mr.edgeR = MEDIPS.meth(MSet1 = MeDIP_AV, MSet2 = MeDIP_C, CSet = CS, p.adj = "none", diff.method = "edgeR", MeDIP = F, CNV = F, minRowSum = 10) Then I eliminate the windows that have no methylation coverage in the mr.edgeR (p.adj="none") using this: mr.edgeR <- mr.edgeR[mr.edgerR$MSets2.counts.mean != c("0"), ] and now I wanna do the manual FDR correction in "mr.edgeR" But I don´t know how.<font face="sans-serif, Arial, Verdana, Trebuchet MS"> </font> ________________________________ Post tags: R, Medips, edgeR You may reply via email or visit How to do FDR p.adj manually on "mr.edgeR object" from MEDIPS package?
ADD COMMENTlink written 3.1 years ago by Lukas Chavez510
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 210 users visited in the last hour