[Bioc-devel] Problem with "RGChannelSetExtended" class form minfi
Hi,
In minfi (1.20.2), in current release version Bioconductor 3.4, the
"RGChannelSetExtended" class is defined as
> getClass("RGChannelSetExtended")
Class "RGChannelSetExtended" [package "minfi"]
Slots:
Name: assayData phenoData featureData experimentData
annotationprotocolData .__classVersion__
Class: AssayData AnnotatedDataFrame AnnotatedDataFrameMIAxE
character AnnotatedDataFrame Versions
Extends:
Class "RGChannelSet", directly
Class "eSet", by class "RGChannelSet", distance 2
Class "VersionedBiobase", by class "RGChannelSet", distance 3
Class "Versioned", by class "RGChannelSet", distance 4
>
But in minfi (1.21.5), in the development version Bioconductor 3.5, the
"RGChannelSetExtended" class is defined as
> getClass("RGChannelSetExtended")
Class "RGChannelSetExtended" [package "minfi"]
Slots:
Name: annotation colData assays NAMES elementMetadata
metadata
Class: character DataFrame Assays character_OR_NULL DataFrame
list
Extends:
Class "RGChannelSet", directly
Class "SummarizedExperiment", by class "RGChannelSet", distance 2
Class "Vector", by class "RGChannelSet", distance 3
Class "Annotated", by class "RGChannelSet", distance 4
Now to make a new package, which class definition I need to use ?
And also , for dependency some other packages (wateRmelon, ChAMP), in their
development version Bioconductor 3.5, still using the old definition of
"RGChannelSetExtended".
If so, how to solve the problem ?
Tanvir Ahamed
Göteborg, Sweden | mashra...@yahoo.com
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Problem with champ.load ( wateRmelon::beadcount function )
Dear Yuan Tian,
Thank you very much for your mail .
I have already add a session info with the previous mail.
Problem arise in your script "champ.load.R" line 70 ( bc=beadcount(rgSet) ).
"beadcount" belongs to package "wateRmelon".
In "beadcount" function from line 3 (nb <- assayDataElement(x, "NBeads"))
problem arise !!
I am using :
R version 3.4.0 alpha (2017-03-28 r72427)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Biobase (2.35.1), minfi (1.21.5), wateRmelon (1.19.3)
Yes you are right. minfi has change their class definition for
"RGChannelSetExtended"
In my current version of R,
> getClass("RGChannelSetExtended")
Class "RGChannelSetExtended" [package "minfi"]
Slots:
Name: annotation colData assays NAMES elementMetadata
metadata
Class: characterDataFrame Assays character_OR_NULL DataFrame
list
Extends:
Class "RGChannelSet", directly
Class "SummarizedExperiment", by class "RGChannelSet", distance 2
Class "Vector", by class "RGChannelSet", distance 3
Class "Annotated", by class "RGChannelSet", distance 4
but in
R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)
minfi (1.20.2)
> getClass("RGChannelSetExtended")
Class "RGChannelSetExtended" [package "minfi"]
Slots:
Name: assayData phenoData featureData experimentData
annotationprotocolData .__classVersion__
Class: AssayData AnnotatedDataFrame AnnotatedDataFrame MIAxE
character AnnotatedDataFrame Versions
Extends:
Class "RGChannelSet", directly
Class "eSet", by class "RGChannelSet", distance 2
Class "VersionedBiobase", by class "RGChannelSet", distance 3
Class "Versioned", by class "RGChannelSet", distance 4
>
No "assayData" is present in present version of minfi !!
Can anybody suggest how to solve the problem ?
Tanvir Ahamed
Göteborg, Sweden | mashra...@yahoo.com
From: Tian Yuan
Sent: Thursday, 30 March 2017, 7:35
Subject: Re: Problem with champ.load
Below is my Test Code:
> testDir=system.file("extdata",package="ChAMPdata")
> myLoad <- champ.load(testDir,arraytype="450K")
[===]
[ ChAMP.LOAD START >]
-
Loading data from
/home/tianyuan/R/x86_64-pc-linux-gnu-library/3.3/ChAMPdata/extdata
[read.metharray.sheet] Found the following CSV files:
[1]
"/home/tianyuan/R/x86_64-pc-linux-gnu-library/3.3/ChAMPdata/extdata/lung_test_set.csv"
Loading required package: IlluminaHumanMethylation450kmanifest
<< Read DataSet Success. >>
The fraction of failed positions per sample
(You may need to delete samples with high proportion of failed
probes
):
Failed CpG Fraction.
C1 0.0013429122
C2 0.0022162171
C3 0.0003563249
C4 0.0002842360
T1 0.0003831007
T2 0.0011946152
T3 0.0014953286
T4 0.0015447610
Filtering probes with a detection p-value above 0.01 in one or more samples has
removed 2728 probes from the analysis. If a large number of probes have been
removed, ChAMP suggests you to identify potentially bad samples.
<< Filter DetP Done. >>
Filtering probes with a beadcount <3 in at least 5% of samples, has removed
9291 from the analysis.
<< Filter Beads Done. >>
Filtering non-cg probes, has removed 2959 from the analysis.
<< Filter NoCG Done. >>
Using general 450K SNP list for filtering.
Filtering probes with SNPs as identified in Zhou's Nucleic Acids Research
Paper, 2016, has removed 49231 from the analysis.
<< Filter SNP Done. >>
Filtering probes that align to multiple locations as identified in Nordlund et
al, has removed 7003 from the analysis.
<< Filter MultiHit Done. >>
Filtering probes on the X or Y chromosome has removed 9917 from the analysis.
<< Filter XY chromosome Done. >>
[Beta value is selected as output.]
Zeros in your dataset have been replaced with 0.01
The analysis will be proceed with 404383 probes and 8 samples.
[< ChAMP.LOAD END >>]
[===]
[You may want to process champ.QC() next.]
Best
Yuan Tian
On Thu, 30 Mar 2017 at 12:02 Tian Yuan wrote:
Hello Tanvir:
>
>
>The error looks wired because seems no one reported that before, I guess it's
>a problem caused by version of Bioba, whihc is a bug in minfi, which is used
>by ChAMP. The problem is the latest version minfi is conflict with old version
>Biobase. The solution is replace your current Biobase package with the latest
>version (2.34), then it should be OK.
>
>Please try it see if it works. You are using Demo data, which should be
>correct as I tried now.
>
>
>Best
>Yuan Tian
>
wrote:
>
>Hi,
>>I am writing the following commend and get the following error.
>>Can you ple
[Bioc-devel] Problem with champ.load (Package ChAMP)
Hi,
I am writing the following command and get the following error.
Can you please look into the issue ?
> testDir=system.file("extdata",package="ChAMPdata")
> myLoad <- champ.load(testDir,arraytype="450K")
[===]
[ ChAMP.LOAD START >]
-
Loading data from C:/Program Files/R/R-3.4.0alpha/library/ChAMPdata/extdata
[read.metharray.sheet] Found the following CSV files:
[1] "C:/Program
Files/R/R-3.4.0alpha/library/ChAMPdata/extdata/lung_test_set.csv"
Loading required package: IlluminaHumanMethylation450kmanifest
<< Read DataSet Success. >>
The fraction of failed positions per sample
(You may need to delete samples with high proportion of failed probes
):
Failed CpG Fraction.
C1 0.0013429122
C2 0.0022162171
C3 0.0003563249
C4 0.0002842360
T1 0.0003831007
T2 0.0011946152
T3 0.0014953286
T4 0.0015447610
Filtering probes with a detection p-value above 0.01 in one or more samples has
removed 2728 probes from the analysis. If a large number of probes have been
removed, ChAMP suggests you to identify potentially bad samples.
<< Filter DetP Done. >>
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'assayData' for signature
'"RGChannelSetExtended"'
>
> sessionInfo()
R version 3.4.0 alpha (2017-03-28 r72427)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=Bangla_Bangladesh.1252 LC_CTYPE=Bangla_Bangladesh.1252
LC_MONETARY=Bangla_Bangladesh.1252
[4] LC_NUMERIC=C LC_TIME=Bangla_Bangladesh.1252
attached base packages:
[1] splines stats4 parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] IlluminaHumanMethylation450kmanifest_0.4.0 ChAMP_2.6.0
[3] IlluminaHumanMethylationEPICmanifest_0.3.0
Illumina450ProbeVariants.db_1.11.0
[5] DMRcate_1.11.2 DMRcatedata_1.10.1
[7] DSS_2.15.0 bsseq_1.11.0
[9] FEM_3.3.1 graph_1.53.0
[11] org.Hs.eg.db_3.4.0 impute_1.49.0
[13] igraph_1.0.1 corrplot_0.77
[15] marray_1.53.0 limma_3.31.19
[17] Matrix_1.2-9 AnnotationDbi_1.37.4
[19] ChAMPdata_2.6.0 minfi_1.21.5
[21] bumphunter_1.15.0 locfit_1.5-9.1
[23] iterators_1.0.8 foreach_1.4.3
[25] Biostrings_2.43.6 XVector_0.15.2
[27] SummarizedExperiment_1.5.7 DelayedArray_0.1.7
[29] matrixStats_0.51.0 Biobase_2.35.1
[31] GenomicRanges_1.27.23 GenomeInfoDb_1.11.9
[33] IRanges_2.9.19 S4Vectors_0.13.15
[35] BiocGenerics_0.21.3
loaded via a namespace (and not attached):
[1] R.utils_2.5.0
IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
[3] RSQLite_1.1-2 htmlwidgets_0.8
[5] trimcluster_0.1-2 grid_3.4.0
[7] BiocParallel_1.9.5 munsell_0.4.3
[9] codetools_0.2-15 preprocessCore_1.37.0
[11] statmod_1.4.29 colorspace_1.3-2
[13] fastICA_1.2-0 BiocInstaller_1.25.3
[15] knitr_1.15.1 robustbase_0.92-7
[17] JADE_2.0-0 isva_1.9
[19] GenomeInfoDbData_0.99.0 biovizBase_1.23.2
[21] diptest_0.75-7 R6_2.2.0
[23] doParallel_1.0.10 illuminaio_0.17.0
[25] clue_0.3-53 flexmix_2.3-13
[27] bitops_1.0-6 reshape_0.8.6
[29] assertthat_0.1
IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
[31] scales_0.4.1 nnet_7.3-12
[33] gtable_0.2.0 methylumi_2.21.0
[35] sva_3.23.0 ensembldb_1.99.12
[37] genefilter_1.57.0 rtracklayer_1.35.9
[39] lazyeval_0.2.0 acepack_1.4.1
[41] GEOquery_2.41.0 dichromat_2.0-0
[43] checkmate_1.8.2 yaml_2.1.14
[45] reshape2_1.4.2
GenomicFeatures_1.27.10
[47] backports_1.0.5 httpuv_1.3.3
[49] qvalue_2.7.0 Hmisc_4.0-2
[51] tools_3.4.0
[Bioc-devel] Problem to install bioconductor for R devel (3.5)
Hi,
I have install development version of r from
https://cran.r-project.org/bin/windows/base/rdevel.html
But when i have tried to install Bioconductor, i got following error.
Can any one please explain why ?
It said "Bioconductor does not yet support R version 3.5.0" but why ??
##
> ## try http:// if https:// URLs are not supported
> source("https://bioconductor.org/biocLite.R";)
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
Bioconductor does not yet support R version 3.5.0
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.25.3), R Under development (unstable)
(2017-03-27 r72423).
Installing package(s) ‘Biobase’, ‘IRanges’, ‘AnnotationDbi’
also installing the dependency ‘S4Vectors’
Warning: unable to access index for repository
https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.5:
cannot open URL
'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.5/PACKAGES'
Warning: unable to access index for repository
https://bioconductor.org/packages/3.5/data/annotation/bin/windows/contrib/3.5:
cannot open URL
'https://bioconductor.org/packages/3.5/data/annotation/bin/windows/contrib/3.5/PACKAGES'
Warning: unable to access index for repository
https://bioconductor.org/packages/3.5/data/experiment/bin/windows/contrib/3.5:
cannot open URL
'https://bioconductor.org/packages/3.5/data/experiment/bin/windows/contrib/3.5/PACKAGES'
Warning: unable to access index for repository
https://bioconductor.org/packages/3.5/extra/bin/windows/contrib/3.5:
cannot open URL
'https://bioconductor.org/packages/3.5/extra/bin/windows/contrib/3.5/PACKAGES'
Error in readRDS(dest) : unknown input format
>
Tanvir Ahamed
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
