Comments (4)
This code is being tested on the test machines. It also works on my
machine:
library(minfiDataEPIC)
rgset450k <- convertArray(RGsetEPIC, "IlluminaHumanMethylation450k")
biocValid()
I am thinking that your versions are not in sync., what is the output of
biocValid()
sessionInfo()
My sessionInfo()
is
> sessionInfo()
R version 3.3.1 Patched (2016-08-19 r71122)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra (10.12.1)
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] IlluminaHumanMethylation450kmanifest_0.4.0
[2] minfiDataEPIC_1.0.0
[3] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
[4] IlluminaHumanMethylationEPICmanifest_0.3.0
[5] minfi_1.20.0
[6] bumphunter_1.14.0
[7] locfit_1.5-9.1
[8] iterators_1.0.8
[9] foreach_1.4.3
[10] Biostrings_2.42.0
[11] XVector_0.14.0
[12] SummarizedExperiment_1.4.0
[13] GenomicRanges_1.26.1
[14] GenomeInfoDb_1.10.1
[15] IRanges_2.8.1
[16] S4Vectors_0.12.0
[17] Biobase_2.34.0
[18] BiocGenerics_0.20.0
[19] BiocInstaller_1.24.0
loaded via a namespace (and not attached):
[1] mclust_5.2 base64_2.0 Rcpp_0.12.7
[4] lattice_0.20-33 Rsamtools_1.26.1 digest_0.6.10
[7] R6_2.2.0 plyr_1.8.4 chron_2.3-47
[10] RSQLite_1.0.0 httr_1.2.1 zlibbioc_1.20.0
[13] GenomicFeatures_1.26.0 data.table_1.9.6 annotate_1.52.0
[16] Matrix_1.2-6 preprocessCore_1.36.0 splines_3.3.1
[19] BiocParallel_1.8.1 stringr_1.1.0 RCurl_1.95-4.8
[22] biomaRt_2.30.0 rtracklayer_1.34.1 multtest_2.30.0
[25] pkgmaker_0.22 openssl_0.9.5 GEOquery_2.40.0
[28] quadprog_1.5-5 codetools_0.2-14 matrixStats_0.51.0
[31] XML_3.98-1.5 reshape_0.8.6
GenomicAlignments_1.10.0
[34] MASS_7.3-45 bitops_1.0-6 grid_3.3.1
[37] nlme_3.1-128 xtable_1.8-2 registry_0.3
[40] DBI_0.5-1 magrittr_1.5 stringi_1.1.2
[43] genefilter_1.56.0 doRNG_1.6 limma_3.30.2
[46] nor1mix_1.2-2 RColorBrewer_1.1-2 siggenes_1.48.0
[49] tools_3.3.1 illuminaio_0.16.0 rngtools_1.2.4
[52] survival_2.40-1 AnnotationDbi_1.36.0 beanplot_1.2
On Thu, Nov 10, 2016 at 1:03 PM, ekarlins [email protected] wrote:
When I try to convert an EPIC RGSet to a 450k RGSet using minfi 1.20.0 I
get the following error:rgset450k <- convertArray(RGsetEpic, "IlluminaHumanMethylation450k")
[convertArray] Casting as IlluminaHumanMethylation450k
Error: all(probes1$ProbeSeqA == probes2$ProbeSeqB) is not TRUEIt looks like the problem is in lines 303 and 304 of https://github.com/
kasperdanielhansen/minfi/blob/master/R/combineArrays.RThe code reads:
stopifnot(all(probes1$ProbeSeqA == probes2$ProbeSeqB))
stopifnot(all(probes1$ProbeSeqB == probes2$ProbeSeqA))So currently it's:
A == B
B == AIf you change it to:
A == A
B == BThe code runs as expected.
Is this a typo?Thanks!
Eric—
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Kasper,
I think you are right. The error was from running on our cluster. The function works fine running on my computer.
Below is sessionInfo on our cluster. Thanks!
sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.8 (Final)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
[2] CGRmeth_1.0
[3] FlowSorted.Blood.450k_1.12.0
[4] IlluminaHumanMethylationEPICanno.ilmn10.hg19_0.1.1
[5] IlluminaHumanMethylationEPICmanifest_0.1.1
[6] devtools_1.12.0
[7] IlluminaHumanMethylation450kmanifest_0.4.0
[8] minfi_1.20.0
[9] bumphunter_1.14.0
[10] locfit_1.5-9.1
[11] iterators_1.0.8
[12] foreach_1.4.3
[13] Biostrings_2.42.0
[14] XVector_0.14.0
[15] SummarizedExperiment_1.4.0
[16] GenomicRanges_1.26.1
[17] GenomeInfoDb_1.10.1
[18] IRanges_2.8.1
[19] S4Vectors_0.12.0
[20] Biobase_2.34.0
[21] BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] httr_1.2.1 nor1mix_1.2-2 splines_3.3.0
[4] doRNG_1.6 Rsamtools_1.26.1 RSQLite_1.0.0
[7] lattice_0.20-34 limma_3.30.2 quadprog_1.5-5
[10] chron_2.3-47 digest_0.6.10 RColorBrewer_1.1-2
[13] preprocessCore_1.36.0 Matrix_1.2-7.1 plyr_1.8.4
[16] GEOquery_2.40.0 siggenes_1.48.0 XML_3.98-1.5
[19] biomaRt_2.30.0 genefilter_1.56.0 zlibbioc_1.20.0
[22] xtable_1.8-2 BiocParallel_1.8.1 openssl_0.9.5
[25] annotate_1.52.0 beanplot_1.2 pkgmaker_0.22
[28] withr_1.0.2 GenomicFeatures_1.26.0 survival_2.40-1
[31] magrittr_1.5 mclust_5.2 memoise_1.0.0
[34] nlme_3.1-128 MASS_7.3-45 tools_3.3.0
[37] registry_0.3 data.table_1.9.6 matrixStats_0.51.0
[40] stringr_1.1.0 rngtools_1.2.4 AnnotationDbi_1.36.0
[43] base64_2.0 grid_3.3.0 RCurl_1.95-4.8
[46] bitops_1.0-6 codetools_0.2-15 multtest_2.30.0
[49] DBI_0.5-1 reshape_0.8.6 roxygen2_5.0.1
[52] R6_2.2.0 illuminaio_0.16.0 GenomicAlignments_1.10.0
[55] rtracklayer_1.34.1 stringi_1.1.2 Rcpp_0.12.7
from minfi.
Your annotation packages on your cluster are out of date. Importantly, for
reasons I dont understand, you have
IlluminaHumanMethylationEPICanno.ilmn10.hg19_0.1.1
loaded. You should remove this package from your system. It points to an
old, error filed annotation file released by Illumina. You want
annotation(RGsetEPIC)
to point to
"ilm10b2.hg19"
(see the "b2"?).
Best,
Kasper
On Thu, Nov 10, 2016 at 2:18 PM, ekarlins [email protected] wrote:
Kasper,
I think you are right. The error was from running on our cluster. The
function works fine running on my computer.Below is sessionInfo on our cluster. Thanks!
sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.8 (Final)locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods baseother attached packages:
[1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
[2] CGRmeth_1.0[3] FlowSorted.Blood.450k_1.12.0
[4] IlluminaHumanMethylationEPICanno.ilmn10.hg19_0.1.1
[5] IlluminaHumanMethylationEPICmanifest_0.1.1[6] devtools_1.12.0
[7] IlluminaHumanMethylation450kmanifest_0.4.0
[8] minfi_1.20.0
[9] bumphunter_1.14.0
[10] locfit_1.5-9.1
[11] iterators_1.0.8
[12] foreach_1.4.3
[13] Biostrings_2.42.0
[14] XVector_0.14.0
[15] SummarizedExperiment_1.4.0
[16] GenomicRanges_1.26.1
[17] GenomeInfoDb_1.10.1
[18] IRanges_2.8.1
[19] S4Vectors_0.12.0
[20] Biobase_2.34.0
[21] BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] httr_1.2.1 nor1mix_1.2-2 splines_3.3.0[4] doRNG_1.6 Rsamtools_1.26.1 RSQLite_1.0.0
[7] lattice_0.20-34 limma_3.30.2 quadprog_1.5-5
[10] chron_2.3-47 digest_0.6.10 RColorBrewer_1.1-2
[13] preprocessCore_1.36.0 Matrix_1.2-7.1 plyr_1.8.4
[16] GEOquery_2.40.0 siggenes_1.48.0 XML_3.98-1.5
[19] biomaRt_2.30.0 genefilter_1.56.0 zlibbioc_1.20.0
[22] xtable_1.8-2 BiocParallel_1.8.1 openssl_0.9.5
[25] annotate_1.52.0 beanplot_1.2 pkgmaker_0.22
[28] withr_1.0.2 GenomicFeatures_1.26.0 survival_2.40-1
[31] magrittr_1.5 mclust_5.2 memoise_1.0.0
[34] nlme_3.1-128 MASS_7.3-45 tools_3.3.0
[37] registry_0.3 data.table_1.9.6 matrixStats_0.51.0
[40] stringr_1.1.0 rngtools_1.2.4 AnnotationDbi_1.36.0
[43] base64_2.0 grid_3.3.0 RCurl_1.95-4.8
[46] bitops_1.0-6 codetools_0.2-15 multtest_2.30.0
[49] DBI_0.5-1 reshape_0.8.6 roxygen2_5.0.1
[52] R6_2.2.0 illuminaio_0.16.0 GenomicAlignments_1.10.0
[55] rtracklayer_1.34.1 stringi_1.1.2 Rcpp_0.12.7—
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Kasper,
Thanks so much for your help! I've found the old code that was adding the old annotation to RGsetEPIC.
To be clear if others read this, the minfi function "convertArray" works well. The issue was I made my RGSet using an old annotation file which caused the function to break.
Thank you Kasper for updating minfi so quickly to work with EPIC arrays! It's really impressive!!
best,
Eric
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