Loading beta values into minfi
1
0
Entering edit mode
CC ▴ 10
@cc-8931
Last seen 3.7 years ago
United States

Hi there, 

I have only beta values available to me in a matrix from 450k array data. I am trying to load the values into minfi as a GenomicRatioSet but keep getting the same error:

> ratioSet <- ratioConvert(betaM, what="beta", keepCN=TRUE)

> Error in (function (classes, fdef, mtable)  : unable to find an inherited method for function ‘ratioConvert’ for signature ‘"matrix"’

I tried to make the matrix a dataframe instead and I get the same error except with the word "matrix" replaced with "data.frame". 

I would like to use the getSex check in minfi and this requires loading in the GenomicRatioSet. 

Any help you can provide would be greatly appreciated. 

 

minfi 450k • 1.9k views
ADD COMMENT
1
Entering edit mode
@kasper-daniel-hansen-2979
Last seen 5 months ago
United States
ratioConvert is not the right function, that one converts a MethylSet into a RatioSet, You want to directly create a RatioSet. Do this by tmp = RatioSet(Beta = betaM) (you can also supply CN estimates if you have those.). Then you have to set the annotation correctly, the easiest is to library(minfiData) annotation(tmp) = annotation(MsetEx) Then you convert to GenomicRatioSet by tmp2 = mapToGenome(tmp) Best, Kasper On Thu, Oct 29, 2015 at 3:13 PM, Sally [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Sally <https: support.bioconductor.org="" u="" 8931=""/> wrote Question: > Loading beta values into minfi <https: support.bioconductor.org="" p="" 73941=""/>: > > > Hi there, > > I have only beta values available to me in a matrix from 450k array data. > I am trying to load the values into minfi as a GenomicRatioSet but keep > getting the same error: > > > ratioSet <- ratioConvert(betaM, what="beta", keepCN=TRUE) > > > Error in (function (classes, fdef, mtable) : unable to find an > inherited method for function ‘ratioConvert’ for signature ‘"matrix"’ > > I tried to make the matrix a dataframe instead and I get the same error > except with the word "matrix" replaced with "data.frame". > > I would like to use the getSex check in minfi and this requires loading in > the GenomicRatioSet. > > Any help you can provide would be greatly appreciated. > > > > ------------------------------ > > Post tags: minfi, 450k > > You may reply via email or visit Loading beta values into minfi >
ADD COMMENT
0
Entering edit mode

Thank you so much for your fast and very helpful reply.

ADD REPLY
0
Entering edit mode

Hi Kasper, 

I was able to load the data into a GenomicRatioSet using your advice. However, when I run GetSex, I get the following error - presumably because I do not have CN values available to me. Is there a way around this?

> Error in .getSex(CN = CN, xIndex = xIndex, yIndex = yIndex, cutoff = cutoff) : 

  must provide CN, xIndex, and yIndex

ADD REPLY
0
Entering edit mode
Well, do you have the methylation and unmethylation values or do you only have the beta values? On Tue, Nov 3, 2015 at 12:00 PM, Sally [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Sally <https: support.bioconductor.org="" u="" 8931=""/> wrote Comment: > Loading beta values into minfi > <https: support.bioconductor.org="" p="" 73941="" #74078="">: > > Hi Kasper, > > I was able to load the data into a GenomicRatioSet using your advice. > However, when I run GetSex, I get the following error - presumably because > I do not have CN values available to me. Is there a way around this? > > > Error in .getSex(CN = CN, xIndex = xIndex, yIndex = yIndex, cutoff = > cutoff) : > > must provide CN, xIndex, and yIndex > > ------------------------------ > > Post tags: minfi, 450k > > You may reply via email or visit > C: Loading beta values into minfi >
ADD REPLY
0
Entering edit mode

Just beta values unfortunately.

ADD REPLY
0
Entering edit mode
It is not impossible that you can do sex estimation by considering the beta values on the X-chromosome, since females (in general) ought to have higher methylation because one copy is silenced. But that is not what we have implemented and tested in minfi; to use the existing tools you need the methylation/unmethylation values. Best, Kasper On Tue, Nov 3, 2015 at 12:29 PM, Sally [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Sally <https: support.bioconductor.org="" u="" 8931=""/> wrote Comment: > Loading beta values into minfi > <https: support.bioconductor.org="" p="" 73941="" #74083="">: > > Just beta values unfortunately. > > ------------------------------ > > Post tags: minfi, 450k > > You may reply via email or visit > C: Loading beta values into minfi >
ADD REPLY
0
Entering edit mode

Okay, thank you, that makes sense. I appreciate your assistance.

ADD REPLY

Login before adding your answer.

Traffic: 264 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