Detection p value cut off
4
0
Entering edit mode
@khadeeja-ismail-4711
Last seen 5.6 years ago
Hi Everyone, I'm new to Bioconductor and also microarrays. Currently I'm working on Illumina Human Methylation 450k data. I have done the color adjustments and ssn normalization. Now I need to remove the probes failing a detection p value cut-off. Would be great if someone could tell me the best way to do this. Thanks, Hajja [[alternative HTML version deleted]]
Normalization Normalization • 852 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 15 hours ago
United States
Hi Hajja, On 6/22/2011 7:13 AM, khadeeja ismail wrote: > Hi Everyone, > > I'm new to Bioconductor and also microarrays. Currently I'm working > on Illumina Human Methylation 450k data. I have done the color > adjustments and ssn normalization. Now I need to remove the probes > failing a detection p value cut-off. Would be great if someone could > tell me the best way to do this. The only 'detection p value' that I know of is based on a comparison between the PM and MM probes on an Affy 3' biased chip. Which isn't what you have. So I don't know that there is such a thing for you. In addition, depending on how your analysis will proceed, you might not really want to do much filtering at the outset. For instance, if you are planning to use limma to do your comparisons, you want to keep all but the most aberrant probes when fitting the model. This is because you are using all data to estimate the expected variance of a probe, so if you filter first you may well be biasing this estimate, which is not ideal. Best, Jim > > Thanks, Hajja > > > > [[alternative HTML version deleted]] > > > > > _______________________________________________ Bioconductor mailing > list Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD COMMENT
0
Entering edit mode
Tim Triche ★ 4.2k
@tim-triche-3561
Last seen 13 months ago
United States
is.na(exprs(yourMethyLumiM)[ which(detection(yourMethyLumiM)>0.01, arr.ind=T) ]) = TRUE assuming you use a 0.01 cutoff, that is. On Wed, Jun 22, 2011 at 4:13 AM, khadeeja ismail <hajjja@yahoo.com> wrote: > Hi Everyone, > > I'm new to Bioconductor and also microarrays. Currently I'm working on > Illumina Human Methylation 450k data. I have done the color adjustments and > ssn normalization. Now I need to remove the probes failing a detection p > value cut-off. Would be great if someone could tell me the best way to do > this. > > Thanks, > Hajja > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]
ADD COMMENT
0
Entering edit mode
@khadeeja-ismail-4711
Last seen 5.6 years ago
Tim Triche, Jr. <tim.triche at="" ...=""> writes: > > is.na(exprs(yourMethyLumiM)[ which(detection(yourMethyLumiM)>0.01, > arr.ind=T) ]) = TRUE > > assuming you use a 0.01 cutoff, that is. Thanks Tim, Will try that. Hajja
ADD COMMENT
0
Entering edit mode
@khadeeja-ismail-4711
Last seen 5.6 years ago
Tim Triche, Jr. <tim.triche at="" ...=""> writes: > > is.na(exprs(yourMethyLumiM)[ which(detection(yourMethyLumiM)>0.01, > arr.ind=T) ]) = TRUE > Thanks, Tim and James, for the tips. Just one quick question. When and for what do we actually use the detectionCall function? Hajja
ADD COMMENT
0
Entering edit mode
Probably the same thing as I wrote. detectionCall is a 'lumi' thing, though. (not that there's anything wrong with that) I use methylumi for most of what I'm doing. Not because one is better than the other, I'm just working on raw data instead of GenomeStudio results. So I am more familiar with the functions in methylumi. On Fri, Jun 24, 2011 at 4:46 AM, Hajja <hajjja@yahoo.com> wrote: > Tim Triche, Jr. <tim.triche@...> writes: > > > > > is.na(exprs(yourMethyLumiM)[ which(detection(yourMethyLumiM)>0.01, > > arr.ind=T) ]) = TRUE > > > > Thanks, Tim and James, for the tips. > Just one quick question. When and for what do we actually use the > detectionCall > function? > > Hajja > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]
ADD REPLY

Login before adding your answer.

Traffic: 464 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6