Question

minfi - estimatecellcount function

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AST ▴ 60

@ast-8648

Last seen 2.6 years ago

INDIA

Recently, I am facing a problem while estimating the cell count and also while using Quantile preprocessing in minfi v1.14.0 (R v3.2.2). I have visited the epigenomic forum but found no answer to that.

> estimateCellCounts(rgSet450k, compositeCellType="Blood",cellTypes=c("CD8T","CD4T", "NK","Bcell","Mono","Gran"), returnAll=TRUE, meanPlot=FALSE, verbose=TRUE)
Loading required package: FlowSorted.Blood.450k [estimateCellCounts] Combining user data with reference (flow sorted) data.
Error in combine(rgSet, referenceRGset) :   objects have different annotations: IlluminaHumanMethylation450k, IlluminaHumanMethylation450kilmn12.hg19

Here the problem is there is no such package available at Bioconductor as 'IlluminaHumanMethylation450kanno'. Currently available annotation file is "IlluminaHumanMethylation450kanno.ilmn12.hg19".

> preprocessQuantile(rgSet450k, fixOutliers = TRUE, removeBadSamples = TRUE, badSampleCutoff = 10.5, quantileNormalize = TRUE, stratified = TRUE, mergeManifest = FALSE, sex = NULL, verbose = TRUE)
[preprocessQuantile] Mapping to genome.
Loading required package: IlluminaHumanMethylation450kanno
Error in getAnnotationObject(object) : 
  cannot load annotation package IlluminaHumanMethylation450kanno
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :  there is no package called ‘IlluminaHumanMethylation450kanno’

Can you please suggest a possible way through.
Thanks

minfi illuminahumanmethylation450kanno.ilmn12.hg19 illuminahumanmethylation450k.db • 2.3k views

ADD COMMENT • link updated 9.3 years ago by Kasper Daniel Hansen ★ 6.5k • written 9.4 years ago by AST ▴ 60

Dan Tenenbaum · Answer 1 · 2015-08-19

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Kasper Daniel Hansen ★ 6.5k

@kasper-daniel-hansen-2979

Last seen 18 months ago

United States

Your rgset450k is very old. You can fix this either by 1) recreate your rgset450k object 2) do rgset450k = updateObject(rgset450k) 3) (a bit dangeorus) rgset450k@annotation = RGsetEx@annotation (where RGsetEx comes from minfiData). Option (2) is the recommended one, and I am pretty sure it should fix it, but I could be remembering it wrongly; its a long time since this change happened. Kasper

ADD COMMENT • link updated 9.3 years ago by Dan Tenenbaum ★ 8.2k • written 9.3 years ago by Kasper Daniel Hansen ★ 6.5k

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I have the same problem. Evrything worked fine until yesterday and today I get the following error message when I try to use preprocessFunnorm function in minfi (see below in bold). I have tried the first 2 fixes you suggested (no luck!). Are you able to think of anything else?

Regards,

Poojitha

rgSet_blood_funnorm<-preprocessFunnorm(rgSet_blood)
[preprocessFunnorm] Background and dye bias correction with noob
Loading required package: IlluminaHumanMethylation450kanno
Error in getAnnotationObject(object) :
cannot load annotation package IlluminaHumanMethylation450kanno
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘IlluminaHumanMethylation450kanno’

ADD REPLY • link 7.2 years ago poojitha.stemcell ▴ 10

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What is the output of annotation(rgSet_blood) sessionInfo() (last one after the error). When did you create this rgSet - a long time ago, recently or just now? Best, Kasper On Wed, Oct 25, 2017 at 6:12 AM, poojitha.stemcell [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User poojitha.stemcell <https: support.bioconductor.org="" u="" 11859=""/> wrote Comment: > minfi - estimatecellcount function > <https: support.bioconductor.org="" p="" 71225="" #102116="">: > > I have the same problem. Evrything worked fine until yesterday and today I > get the following error message when I try to use preprocessFunnorm > function in minfi (see below in bold). I have tried the first 2 fixes you > suggested (no luck!). Are you able to think of anything else? > > Regards, > > Poojitha > > > > > > > > > *rgSet_blood_funnorm<-preprocessFunnorm(rgSet_blood) [preprocessFunnorm] > Background and dye bias correction with noob Loading required package: > IlluminaHumanMethylation450kanno Error in getAnnotationObject(object) : > cannot load annotation package IlluminaHumanMethylation450kanno In > addition: Warning message: In library(package, lib.loc = lib.loc, > character.only = TRUE, logical.return = TRUE, : there is no package > called ‘IlluminaHumanMethylation450kanno’* > > ------------------------------ > > Post tags: minfi, illuminahumanmethylation450kanno.ilmn12.hg19, > illuminahumanmethylation450k.db > > You may reply via email or visit https://support.bioconductor. > org/p/71225/#102116 >

ADD REPLY • link 7.2 years ago Kasper Daniel Hansen ★ 6.5k