estimateCellCounts() not working

[MeganBreitbach]

I have been trying to get estimateCellCounts() to work, and keep getting a similar error with both 450k and EPIC data. I am currently working through the "hansenlab/tutorial.450k," which is giving the same error.

library(FlowSorted.Blood.450k) cellCounts <- estimateCellCounts(RGSet) [estimateCellCounts] Combining user data with reference (flow sorted) data.

Error in [[<-.data.frame(*tmp*, i, value = c("IlluminaHumanMethylation450k", : replacement has 66 rows, data has 6

EDIT: When the code was altered around line 40 -

combinedRGset <- combineArrays(rgSet, referenceRGset, outType = "IlluminaHumanMethylation450k")

to be

combinedRGset <- combine(rgSet, referenceRGset)

the function worked on methyl450k data, but still will not work for EPIC data that has been converted to 450k data via the convertArray() function.

Any ideas?

[Jfortin1]

Hi Meghan, you're right, it fails on my datasets as well. Let me work on it and fix it asap.

[Jfortin1]

Update: the RGChannelSet objects from the blood reference datasets are old versions and should be updated to be compatible with the current Bioconductor release. We are rewriting a combine() function that will take care of such unfortunate cases; will let you know as soon as updated on GitHub. Thanks again

[MeganBreitbach]

Any status on the update?

[Jfortin1]

Fixed now. Changed are included on GitHub (version 1.19.14).

[kasperdanielhansen]

You can get it from Github now or (hopefully) using biocLite in 2 days.

So we have made some improvements where you should be able to just run estimateCellCounts on your EPIC data directly; conversion to 450k format to use 450k reference data will happen automatically.

Kasper

On Wed, Sep 14, 2016 at 3:20 PM, Jean-Philippe Fortin < notifications@github.com> wrote:

Fixed now. Changes are included on github minfi version 1.19.14

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[MeganBreitbach]

I just tried to use the updated Github estimateCellCounts() function and keep getting this error on both 450k and EPIC data

cellCounts_epic <- estimateCellCounts(RGset_epic) [estimateCellCounts] Combining user data with reference (flow sorted) data.

Error in combine(pDataX, pDataY) : data.frames contain conflicting data: non-conforming colname(s): Slide Called from: combine(pDataX, pDataY)

[kasperdanielhansen]

Show us the output of sessionInfo()

[MeganBreitbach]

sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.6 (El Capitan)

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 methods base

other attached packages: [1] BiocInstaller_1.23.9
[2] FlowSorted.Blood.450k_1.11.0
[3] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.3.0 [4] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 [5] IlluminaHumanMethylationEPICmanifest_0.3.0
[6] IlluminaHumanMethylation450kmanifest_0.4.0
[7] pROC_1.8
[8] matrixStats_0.50.2
[9] pbapply_1.2-2
[10] minfi_1.19.13
[11] bumphunter_1.13.1
[12] locfit_1.5-9.1
[13] iterators_1.0.8
[14] foreach_1.4.3
[15] Biostrings_2.41.4
[16] XVector_0.13.7
[17] SummarizedExperiment_1.3.82
[18] GenomicRanges_1.25.94
[19] GenomeInfoDb_1.9.10
[20] IRanges_2.7.15
[21] S4Vectors_0.11.14
[22] lattice_0.20-34
[23] Biobase_2.33.3
[24] BiocGenerics_0.19.2

loaded via a namespace (and not attached): [1] mclust_5.2 base64_2.0 Rcpp_0.12.7
[4] Rsamtools_1.25.2 digest_0.6.10 R6_2.1.3
[7] plyr_1.8.4 chron_2.3-47 RSQLite_1.0.0
[10] httr_1.2.1 zlibbioc_1.19.0 GenomicFeatures_1.25.16 [13] data.table_1.9.6 annotate_1.51.0 Matrix_1.2-7.1
[16] preprocessCore_1.35.0 splines_3.3.1 BiocParallel_1.7.8
[19] stringr_1.1.0 RCurl_1.95-4.8 biomaRt_2.29.2
[22] rtracklayer_1.33.12 multtest_2.29.0 pkgmaker_0.22
[25] openssl_0.9.4 GEOquery_2.39.3 quadprog_1.5-5
[28] codetools_0.2-14 XML_3.98-1.4 reshape_0.8.5
[31] GenomicAlignments_1.9.6 MASS_7.3-45 bitops_1.0-6
[34] grid_3.3.1 nlme_3.1-128 xtable_1.8-2
[37] registry_0.3 DBI_0.5-1 magrittr_1.5
[40] stringi_1.1.1 genefilter_1.55.2 doRNG_1.6
[43] limma_3.29.21 nor1mix_1.2-2 RColorBrewer_1.1-2
[46] siggenes_1.47.0 tools_3.3.1 illuminaio_0.15.1
[49] rngtools_1.2.4 survival_2.39-5 AnnotationDbi_1.35.4
[52] beanplot_1.2

[kasperdanielhansen]

You need minfi 1.19.14. You have 1.19.13.

On Wed, Sep 14, 2016 at 4:01 PM, Megan notifications@github.com wrote:

sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.6 (El Capitan)

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 methods base

other attached packages: [1] BiocInstaller_1.23.9

[2] FlowSorted.Blood.450k_1.11.0

[3] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.3.0 [4] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 [5] IlluminaHumanMethylationEPICmanifest_0.3.0

[6] IlluminaHumanMethylation450kmanifest_0.4.0

[7] pROC_1.8

[8] matrixStats_0.50.2

[9] pbapply_1.2-2

[10] minfi_1.19.13

[11] bumphunter_1.13.1

[12] locfit_1.5-9.1

[13] iterators_1.0.8

[14] foreach_1.4.3

[15] Biostrings_2.41.4

[16] XVector_0.13.7

[17] SummarizedExperiment_1.3.82

[18] GenomicRanges_1.25.94

[19] GenomeInfoDb_1.9.10

[20] IRanges_2.7.15

[21] S4Vectors_0.11.14

[22] lattice_0.20-34

[23] Biobase_2.33.3

[24] BiocGenerics_0.19.2

loaded via a namespace (and not attached): [1] mclust_5.2 base64_2.0 Rcpp_0.12.7

[4] Rsamtools_1.25.2 digest_0.6.10 R6_2.1.3

[7] plyr_1.8.4 chron_2.3-47 RSQLite_1.0.0

[10] httr_1.2.1 zlibbioc_1.19.0 GenomicFeatures_1.25.16 [13] data.table_1.9.6 annotate_1.51.0 Matrix_1.2-7.1

[16] preprocessCore_1.35.0 splines_3.3.1 BiocParallel_1.7.8

[19] stringr_1.1.0 RCurl_1.95-4.8 biomaRt_2.29.2

[22] rtracklayer_1.33.12 multtest_2.29.0 pkgmaker_0.22

[25] openssl_0.9.4 GEOquery_2.39.3 quadprog_1.5-5

[28] codetools_0.2-14 XML_3.98-1.4 reshape_0.8.5

[31] GenomicAlignments_1.9.6 MASS_7.3-45 bitops_1.0-6

[34] grid_3.3.1 nlme_3.1-128 xtable_1.8-2

[37] registry_0.3 DBI_0.5-1 magrittr_1.5

[40] stringi_1.1.1 genefilter_1.55.2 doRNG_1.6

[43] limma_3.29.21 nor1mix_1.2-2 RColorBrewer_1.1-2

[46] siggenes_1.47.0 tools_3.3.1 illuminaio_0.15.1

[49] rngtools_1.2.4 survival_2.39-5 AnnotationDbi_1.35.4

[52] beanplot_1.2

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[MeganBreitbach]

Got is, but it's still not working.

cellCounts_450 <- estimateCellCounts(RGset_450) [estimateCellCounts] Combining user data with reference (flow sorted) data.

Error in [[<-.data.frame(*tmp*, i, value = c("IlluminaHumanMethylation450k", : replacement has 84 rows, data has 24

cellCounts_epic <- estimateCellCounts(RGset_epic) Loading required package: FlowSorted.Blood.EPIC Error in estimateCellCounts(RGset_epic) : Could not find reference data package for compositeCellType 'Blood' and platform 'EPIC' (inferred package name is 'FlowSorted.Blood.EPIC')

[MeganBreitbach]

When I use convertArray() to covert EPIC to 450k first, the same error with 450k occurs-

cellCounts_epic <- estimateCellCounts(convertedEPIC) [estimateCellCounts] Combining user data with reference (flow sorted) data.

Error in [[<-.data.frame(*tmp*, i, value = c("IlluminaHumanMethylation450k", : replacement has 76 rows, data has 16

[Jfortin1]

Well I still believe you do not have the latest version of the package. How did you install the latest version of the package?

[Jfortin1]

What is your sessionInfo() ?

[MeganBreitbach]

sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.6 (El Capitan)

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 methods base

other attached packages: [1] BiocInstaller_1.23.9
[2] FlowSorted.Blood.450k_1.11.0
[3] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.3.0 [4] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 [5] IlluminaHumanMethylationEPICmanifest_0.3.0
[6] IlluminaHumanMethylation450kmanifest_0.4.0
[7] pROC_1.8
[8] matrixStats_0.50.2
[9] pbapply_1.2-2
[10] minfi_1.19.14
[11] bumphunter_1.13.1
[12] locfit_1.5-9.1
[13] iterators_1.0.8
[14] foreach_1.4.3
[15] Biostrings_2.41.4
[16] XVector_0.13.7
[17] SummarizedExperiment_1.3.82
[18] GenomicRanges_1.25.94
[19] GenomeInfoDb_1.9.10
[20] IRanges_2.7.15
[21] S4Vectors_0.11.14
[22] lattice_0.20-34
[23] Biobase_2.33.3
[24] BiocGenerics_0.19.2

loaded via a namespace (and not attached): [1] mclust_5.2 base64_2.0 Rcpp_0.12.7
[4] Rsamtools_1.25.2 digest_0.6.10 R6_2.1.3
[7] plyr_1.8.4 chron_2.3-47 RSQLite_1.0.0
[10] httr_1.2.1 zlibbioc_1.19.0 GenomicFeatures_1.25.16 [13] data.table_1.9.6 annotate_1.51.0 Matrix_1.2-7.1
[16] preprocessCore_1.35.0 splines_3.3.1 BiocParallel_1.7.8
[19] stringr_1.1.0 RCurl_1.95-4.8 biomaRt_2.29.2
[22] rtracklayer_1.33.12 multtest_2.29.0 pkgmaker_0.22
[25] openssl_0.9.4 GEOquery_2.39.3 quadprog_1.5-5
[28] codetools_0.2-14 XML_3.98-1.4 reshape_0.8.5
[31] GenomicAlignments_1.9.6 MASS_7.3-45 bitops_1.0-6
[34] grid_3.3.1 nlme_3.1-128 xtable_1.8-2
[37] registry_0.3 DBI_0.5-1 magrittr_1.5
[40] stringi_1.1.1 genefilter_1.55.2 doRNG_1.6
[43] limma_3.29.21 nor1mix_1.2-2 RColorBrewer_1.1-2
[46] siggenes_1.47.0 tools_3.3.1 illuminaio_0.15.1
[49] rngtools_1.2.4 survival_2.39-5 AnnotationDbi_1.35.4
[52] beanplot_1.2

[MeganBreitbach]

I downloaded the ZIP file from https://github.com/Bioconductor-mirror/minfi

[Jfortin1]

Weird. I would try library(devtools) install_github("kasperdanielhansen/minfi") and see if it works

[MeganBreitbach]

It works when downloaded that way. Thanks!

[kasperdanielhansen]

Solved; closing.