Question

mapToGenome minfi package

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Asma rabe ▴ 290

@asma-rabe-4697

Last seen 6.2 years ago

Japan

Hi,

I am using minfi 1.8.9

I loaded a matrix of beta values into minfi and try to annotate to genome as follows:

tmp = RatioSet(Beta = BMtrx)
annotation(tmp) = annotation(MsetEx)
tmp2 = mapToGenome(tmp)

I got the following error which indicates that an argument is missed in the function:

Error in .local(object, ...) :
object does not contain 'CN' amongst assay slots

Any idea?

Thank you in advance

minfi • 1.1k views

ADD COMMENT • link updated 8.0 years ago by Kasper Daniel Hansen ★ 6.5k • written 8.0 years ago by Asma rabe ▴ 290

score 0 · Answer 1 · 2016-05-17

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Kasper Daniel Hansen ★ 6.5k

@kasper-daniel-hansen-2979

Last seen 10 months ago

United States

1. Make sure that everything has the same version by running biocValid() and see if it returns TRUE. 2. Check that the object is valid, by running validObject(tmp) If the problem still persists, send me the BMtrx offline and Ill have a look (its good enough to just get 2-4 columns of the matrix). Best, Kasper On Tue, May 17, 2016 at 2:29 AM, Asma rabe [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Asma rabe <https: support.bioconductor.org="" u="" 4697=""/> wrote Question: > mapToGenome minfi package <https: support.bioconductor.org="" p="" 82704=""/>: > > Hi, > > I am using minfi 1.8.9 > > I loaded a matrix of beta values into minfi and try to annotate to genome > as follows: > > tmp = RatioSet(Beta = BMtrx) > annotation(tmp) = annotation(MsetEx) > tmp2 = mapToGenome(tmp) > > I got the following error which indicates that an argument is missed in > the function: > > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function 'Rle' for signature > '"NULL", "missing"' > > Any idea? > > Thank you in advance > > ------------------------------ > > Post tags: minfi > > You may reply via email or visit mapToGenome minfi package >

ADD COMMENT • link 8.0 years ago Kasper Daniel Hansen ★ 6.5k

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Thanks Kasper for the quick response. I checked that every thing has the same version and the object is valid.

ADD REPLY • link 8.0 years ago Asma rabe ▴ 290

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Then I think I need a couple of columns of the beta matrix object, to be of any help. Kasper On Tue, May 17, 2016 at 9:22 PM, Asma rabe [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Asma rabe <https: support.bioconductor.org="" u="" 4697=""/> wrote Comment: > mapToGenome minfi package > <https: support.bioconductor.org="" p="" 82704="" #82757="">: > > Thanks Kasper for the quick response. I checked that every thing has the > same version and the object is valid. > > ------------------------------ > > Post tags: minfi > > You may reply via email or visit > C: mapToGenome minfi package >