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Question: Loading beta values into minfi
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gravatar for CC
2.1 years ago by
CC10
United States
CC10 wrote:

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. 

 

ADD COMMENTlink modified 2.1 years ago by Kasper Daniel Hansen6.3k • written 2.1 years ago by CC10
1
gravatar for Kasper Daniel Hansen
2.1 years ago by
United States
Kasper Daniel Hansen6.3k wrote:
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 COMMENTlink written 2.1 years ago by Kasper Daniel Hansen6.3k

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

ADD REPLYlink written 2.1 years ago by CC10

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 REPLYlink written 2.1 years ago by CC10
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 REPLYlink written 2.1 years ago by Kasper Daniel Hansen6.3k

Just beta values unfortunately.

ADD REPLYlink written 2.1 years ago by CC10
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 REPLYlink written 2.1 years ago by Kasper Daniel Hansen6.3k

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

ADD REPLYlink written 2.1 years ago by CC10
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