Can't guess EPIC array type in minfi

[XY Zhang]

I have some illumina EPIC array data. When using read.metharray.exp function in minfi package, it returned unknown array type, so the following steps can not applied such as detectionP. 

> RGSet <- read.metharray.exp(base = baseDir, targets = targets, recursive = T)

> RGSet

RGChannelSet (storageMode: lockedEnvironment)

assayData: 1051943 features, 8 samples 

  element names: Green, Red 

An object of class 'AnnotatedDataFrame'

  sampleNames: 201194000210_R01C01 201194000210_R02C01 ...

    201194000210_R08C01 (8 total)

  varLabels: Array kexuID ... filenames (21 total)

  varMetadata: labelDescription

Annotation

  array: Unknown

  annotation: Unknown

> sessionInfo()

R version 3.3.3 (2017-03-06)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X El Capitan 10.11.6

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:

[1] stats4    parallel  stats     graphics  grDevices utils     datasets 

[8] methods   base     

other attached packages:

 [1] limma_3.30.13                                     

 [2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0

 [3] minfi_1.20.2                                      

 [4] bumphunter_1.14.0                                 

 [5] locfit_1.5-9.1                                    

 [6] iterators_1.0.8                                   

 [7] foreach_1.4.3                                     

 [8] Biostrings_2.42.1                                 

 [9] XVector_0.14.1                                    

[10] SummarizedExperiment_1.4.0                        

[11] GenomicRanges_1.26.4                              

[12] GenomeInfoDb_1.10.3                               

[13] IRanges_2.8.2                                     

[14] S4Vectors_0.12.2                                  

[15] Biobase_2.34.0                                    

[16] BiocGenerics_0.20.0                               

loaded via a namespace (and not attached):

 [1] genefilter_1.56.0        splines_3.3.3            lattice_0.20-34         

 [4] beanplot_1.2             rtracklayer_1.34.2       GenomicFeatures_1.26.3  

 [7] XML_3.98-1.5             survival_2.41-2          DBI_0.6                 

[10] BiocParallel_1.8.1       RColorBrewer_1.1-2       registry_0.3            

[13] rngtools_1.2.4           doRNG_1.6                matrixStats_0.51.0      

[16] plyr_1.8.4               stringr_1.2.0            pkgmaker_0.22           

[19] zlibbioc_1.20.0          codetools_0.2-15         memoise_1.0.0           

[22] biomaRt_2.30.0           AnnotationDbi_1.36.2     illuminaio_0.16.0       

[25] preprocessCore_1.36.0    Rcpp_0.12.10             xtable_1.8-2            

[28] openssl_0.9.6            base64_2.0               annotate_1.52.1         

[31] Rsamtools_1.26.1         digest_0.6.12            stringi_1.1.3           

[34] nor1mix_1.2-2            grid_3.3.3               GEOquery_2.40.0         

[37] quadprog_1.5-5           tools_3.3.3              bitops_1.0-6            

[40] magrittr_1.5             siggenes_1.48.0          RCurl_1.95-4.8          

[43] RSQLite_1.1-2            MASS_7.3-45              Matrix_1.2-8            

[46] data.table_1.10.4        httr_1.2.1               reshape_0.8.6           

[49] R6_2.2.0                 mclust_5.2.3             nlme_3.1-131            

[52] GenomicAlignments_1.10.1 multtest_2.30.0  

[XY Zhang]

I have installed the EPIC manifest and annotation package, and restarted Studio. But same results:

> RGSet

RGChannelSet (storageMode: lockedEnvironment)

assayData: 1051943 features, 8 samples 

  element names: Green, Red 

An object of class 'AnnotatedDataFrame'

  sampleNames: 201194000210_R01C01 201194000210_R02C01 ...

    201194000210_R08C01 (8 total)

  varLabels: Array kexuID ... filenames (21 total)

  varMetadata: labelDescription

Annotation

  array: Unknown

  annotation: Unknown

> sessionInfo()

R version 3.3.3 (2017-03-06)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X El Capitan 10.11.6

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:

[1] stats4    parallel  stats     graphics  grDevices utils     datasets 

[8] methods   base     

other attached packages:

 [1] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0

 [2] IlluminaHumanMethylationEPICmanifest_0.3.0         

 [3] limma_3.30.13                                      

 [4] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 

 [5] minfi_1.20.2                                       

 [6] bumphunter_1.14.0                                  

 [7] locfit_1.5-9.1                                     

 [8] iterators_1.0.8                                    

 [9] foreach_1.4.3                                      

[10] Biostrings_2.42.1                                  

[11] XVector_0.14.1                                     

[12] SummarizedExperiment_1.4.0                         

[13] GenomicRanges_1.26.4                               

[14] GenomeInfoDb_1.10.3                                

[15] IRanges_2.8.2                                      

[16] S4Vectors_0.12.2                                   

[17] Biobase_2.34.0                                     

[18] BiocGenerics_0.20.0                                

loaded via a namespace (and not attached):

 [1] mclust_5.2.3             base64_2.0               Rcpp_0.12.10            

 [4] lattice_0.20-34          Rsamtools_1.26.1         digest_0.6.12           

 [7] R6_2.2.0                 plyr_1.8.4               RSQLite_1.1-2           

[10] httr_1.2.1               zlibbioc_1.20.0          GenomicFeatures_1.26.3  

[13] data.table_1.10.4        annotate_1.52.1          Matrix_1.2-8            

[16] preprocessCore_1.36.0    splines_3.3.3            BiocParallel_1.8.1      

[19] stringr_1.2.0            RCurl_1.95-4.8           biomaRt_2.30.0          

[22] rtracklayer_1.34.2       multtest_2.30.0          pkgmaker_0.22           

[25] openssl_0.9.6            GEOquery_2.40.0          quadprog_1.5-5          

[28] codetools_0.2-15         matrixStats_0.51.0       XML_3.98-1.5            

[31] reshape_0.8.6            GenomicAlignments_1.10.1 MASS_7.3-45             

[34] bitops_1.0-6             grid_3.3.3               nlme_3.1-131            

[37] xtable_1.8-2             registry_0.3             DBI_0.6                 

[40] magrittr_1.5             stringi_1.1.3            genefilter_1.56.0       

[43] doRNG_1.6                nor1mix_1.2-2            RColorBrewer_1.1-2      

[46] siggenes_1.48.0          tools_3.3.3              illuminaio_0.16.0       

[49] rngtools_1.2.4           survival_2.41-2          AnnotationDbi_1.36.2    

[52] beanplot_1.2             memoise_1.0.0   

[Tim Triche, Jr.]

can you make one of the IDATs available?

[Kasper Daniel Hansen]

This is fixed in minfi devel on Github which will be pushed to Bioconductor in a couple of days.

You can fix the problem by manually setting annotation(RGset); look for the data in minfiDataEPIC for an example of the value.

Best,

Kasper

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[XY Zhang]

Thanks. I shared one dataset in Google Drive: 

https://drive.google.com/open?id=0B7f5u_enrqI6MUJibUx6Xy13ZUE

https://drive.google.com/open?id=0B7f5u_enrqI6RVRmdkNSV2hZcjg

[XY Zhang]

Hi Kasper,

I tried annotation(RGSet) = c("IlluminaHumanMethylationEPICanno", "ilm10b2.hg19"), or annotation(RGSet) = c("IlluminaHumanMethylationEPIC", "ilm10b2.hg19"), but both failed:

> getAnnotation(RGSet)

Error in .getAnnotationString(object@annotation) : 

  unable to get the annotation string for this object

It seems the annotation parameters what I set were false one for EPIC. What are the correct ones? 

Thanks

Best,

Xinyu Zhang

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[Kasper Daniel Hansen]

It needs to be a named vector.  You need to add names
  c(array = "IlluminaHumanMethylationEPICanno", annotation = "ilm10b2.hg19")

Best,

Kasper

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[XY Zhang]

Hi Kasper,

Now the function works, but there are still troubles in the further steps:

I used "annotation(RGSet) = c(array = "IlluminaHumanMethylationEPIC", annotation = "ilm10b2.hg19")" to make sure it find the proper manifest package. 

> RGSet

RGChannelSet (storageMode: lockedEnvironment)

assayData: 1051943 features, 8 samples 

  element names: Green, Red 

An object of class 'AnnotatedDataFrame'

  sampleNames: 201194000210_R01C01 201194000210_R02C01 ...

    201194000210_R08C01 (8 total)

  varLabels: Array kexuID ... filenames (21 total)

  varMetadata: labelDescription

Annotation

  array: IlluminaHumanMethylationEPIC

  annotation: ilm10b2.hg19

> detP <- detectionP(RGSet)

Error in r[TypeI.Red$AddressA, i] : subscript out of bounds

I think it may be because my array version (probe numbers) is a little different with the current manifest and annotation version in bioconductor? So that the function can not deduct the array type, and also report errors in detectionP step. I am not sure about it.

Best,

Xinyu

[Kasper Daniel Hansen]

I cannot reproduce this error with the file(s) you sent.

Best,

Kasper

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[XY Zhang]

So it should be R and minfi version problem. I will update them first and try it again. Thank you!

Best,

Xinyu

[XY Zhang]

Finally it is not a problem with R and minfi version.

I got the following error when processing large scale of samples:

...

201172520052_R01C01 "Unknown"                      "1051943"

201172520053_R01C01 "Unknown"                      "1051943"

201172520054_R01C01 "Unknown"                      "1051943"

201172540058_R01C01 "Unknown"                      "1051943"

201134840069_R01C01 "IlluminaHumanMethylationEPIC" "1052641"

201134840076_R01C01 "IlluminaHumanMethylationEPIC" "1052641"

201134840080_R01C01 "IlluminaHumanMethylationEPIC" "1052641"

201134840084_R01C01 "IlluminaHumanMethylationEPIC" "1052641"

201172220032_R01C01 "Unknown"                      "1051943"

201172220046_R01C01 "Unknown"                      "1051943"

201172220053_R01C01 "Unknown"                      "1051943"

201172550049_R02C01 "Unknown"                      "1051943"

201172520052_R02C01 "Unknown"                      "1051943"

201172520053_R02C01 "Unknown"                      "1051943"

201172520054_R02C01 "Unknown"                      "1051943"

201172540058_R02C01 "Unknown"                      "1051943"

201134840069_R02C01 "IlluminaHumanMethylationEPIC" "1052641"

201134840076_R02C01 "IlluminaHumanMethylationEPIC" "1052641"

201134840080_R02C01 "IlluminaHumanMethylationEPIC" "1052641"

201134840084_R02C01 "IlluminaHumanMethylationEPIC" "1052641"

...

[read.metharray] Creating data matrices ...

Error in read.metharray(files, extended = extended, verbose = verbose,  :

  [read.metharray] Trying to parse different IDAT files, of different size and type.

Calls: read.metharray.exp -> read.metharray

Execution halted

Some datasets were correctly annotated and some not with a different probe number.

Similar problem was described at https://support.bioconductor.org/p/94226/

It seems that is not related with array data quality, yet the problem still unknown. 

Best,

Xinyu 

[Kasper Daniel Hansen]

This problem is solved in minfi devel, certainly minfi >= 1.21.6

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[XY Zhang]

Thank you, Kasper. 

I found the version in minfi development version (https://bioconductor.org/packages/devel/bioc/html/minfi.html), and it works well with force = T parameter. 

[Marie Loh]

Hi all

I get the same error too

> detP <- detectionP(RGSet)

Error in r[TypeI.Red$AddressA, i] : subscript out of bounds

My code was working previously and I just reinstalled the minfi library via biocLite so I am not sure what's the problem...?

Cheers,

Marie

[Kasper Daniel Hansen]

If you have the newest minfi library (and I might add it is not clear if this is true, since you don't tell us what version you have), I would also recreate the RGset by reading it again.  

Best,

Kasper

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[Marie Loh]

Works now, thanks! 

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