Question

Removing samples from S4 object (in lumi)

0

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Chi Hong • 0

@chi-hong-7095

Last seen 8.9 years ago

United States

How do I remove (failed) samples from my LumiBatch object?

I've detected outlying samples from the various QC plots generated by lumiQ (actually, lumiR). I know their sample names. I'd like to remove them before normalizing the data and subsequent analysis.

I tried something like this:

sampleNames(lumiExpr) <- pData(lumiExpr)$sampleID

badsamp = c("5406958048_G","5406958047_I")

toremove = pData(lumiBatch.object)$sampleID %in% badsamp

lumiExpr.new = lumiExpr[ , !toremove]

Got this error message:

The sample names in the controlData don't match sampleNames(object).
Warning message:
In lumiExpr[ , !toremove] :
The controlData slot does not match the sampleNames.
The subsetting did not execute on controlData.

Is there a better way to do this?

lumi S4 • 2.9k views

ADD COMMENT • link 9.8 years ago Chi Hong • 0

1

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Levi Waldron ★ 1.1k

@levi-waldron-3429

Last seen 27 days ago

CUNY Graduate School of Public Health a…

Pan, I think this is a bug in how lumi subsets from logical vectors, not user error - for example:

> library(lumi)

> data(example.lumi)

> dim(example.lumi)

Features Samples

8000 4

> example.lumi[, 1:3]

Summary of data information:

Illumina Inc. BeadStudio version 1.4.0.1

Normalization = none

Array Content = 11188230_100CP_MAGE-ML.XML

Error Model = none

DateTime = 2/3/2005 3:21 PM

Local Settings = en-US

Major Operation History:

submitted finished

1 2007-04-22 00:08:36 2007-04-22 00:10:36

2 2007-04-22 00:10:36 2007-04-22 00:10:38

3 2007-04-22 00:13:06 2007-04-22 00:13:10

4 2007-04-22 00:59:20 2007-04-22 00:59:36

5 2015-03-05 14:32:23 2015-03-05 14:32:23

command lumiVersion

1 lumiR("../data/Barnes_gene_profile.txt") 1.1.6

2 lumiQ(x.lumi = x.lumi) 1.1.6

3 addNuId2lumi(x.lumi = x.lumi, lib = "lumiHumanV1") 1.1.6

4 Subsetting 8000 features and 4 samples. 1.1.6

5 Subsetting 4 samples. 2.18.0

Object Information:

LumiBatch (storageMode: lockedEnvironment)

assayData: 8000 features, 3 samples

element names: beadNum, detection, exprs, se.exprs

protocolData: none

phenoData

sampleNames: A01 A02 B01

varLabels: sampleID label

varMetadata: labelDescription

featureData

featureNames: oZsQEQXp9ccVIlwoQo 9qedFRd_5Cul.ueZeQ ...

33KnLHy.RFaieogAF4 (8000 total)

fvarLabels: TargetID

fvarMetadata: labelDescription

experimentData: use 'experimentData(object)'

Annotation: lumiHumanAll.db

Control Data: Available

QC information: Please run summary(x, 'QC') for details!

> example.lumi[, c(T, T, T, F)]

The sample names in the controlData don't match sampleNames(object).

Summary of data information:

Illumina Inc. BeadStudio version 1.4.0.1

Normalization = none

Array Content = 11188230_100CP_MAGE-ML.XML

Error Model = none

DateTime = 2/3/2005 3:21 PM

Local Settings = en-US

Major Operation History:

submitted finished

1 2007-04-22 00:08:36 2007-04-22 00:10:36

2 2007-04-22 00:10:36 2007-04-22 00:10:38

3 2007-04-22 00:13:06 2007-04-22 00:13:10

4 2007-04-22 00:59:20 2007-04-22 00:59:36

5 2015-03-05 14:32:23 2015-03-05 14:32:23

command lumiVersion

1 lumiR("../data/Barnes_gene_profile.txt") 1.1.6

2 lumiQ(x.lumi = x.lumi) 1.1.6

3 addNuId2lumi(x.lumi = x.lumi, lib = "lumiHumanV1") 1.1.6

4 Subsetting 8000 features and 4 samples. 1.1.6

5 Subsetting 4 samples. 2.18.0

Object Information:

LumiBatch (storageMode: lockedEnvironment)

assayData: 8000 features, 3 samples

element names: beadNum, detection, exprs, se.exprs

protocolData: none

phenoData

sampleNames: A01 A02 B01

varLabels: sampleID label

varMetadata: labelDescription

featureData

featureNames: oZsQEQXp9ccVIlwoQo 9qedFRd_5Cul.ueZeQ ...

33KnLHy.RFaieogAF4 (8000 total)

fvarLabels: TargetID

fvarMetadata: labelDescription

experimentData: use 'experimentData(object)'

Annotation: lumiHumanAll.db

Control Data: Available

QC information: Please run summary(x, 'QC') for details!

Warning message:

In example.lumi[, c(T, T, T, F)] :

The controlData slot does not match the sampleNames.

The subsetting did not execute on controlData.

> sessionInfo()

R version 3.1.2 (2014-10-31)

Platform: x86_64-pc-linux-gnu (64-bit)

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] parallel stats graphics grDevices utils datasets methods

[8] base

other attached packages:

[1] lumi_2.18.0 Biobase_2.26.0 BiocGenerics_0.12.1

loaded via a namespace (and not attached):

[1] affy_1.44.0 affyio_1.34.0 annotate_1.44.0

[4] AnnotationDbi_1.28.1 base64_1.1 base64enc_0.1-2

[7] BatchJobs_1.5 BBmisc_1.9 beanplot_1.2

[10] BiocInstaller_1.16.1 BiocParallel_1.0.3 biomaRt_2.22.0

[13] Biostrings_2.34.1 bitops_1.0-6 brew_1.0-6

[16] BSgenome_1.34.1 bumphunter_1.6.0 checkmate_1.5.1

[19] codetools_0.2-10 colorspace_1.2-5 DBI_0.3.1

[22] digest_0.6.8 doRNG_1.6 fail_1.2

[25] foreach_1.4.2 genefilter_1.48.1 GenomeInfoDb_1.2.4

[28] GenomicAlignments_1.2.2 GenomicFeatures_1.18.3 GenomicRanges_1.18.4

[31] grid_3.1.2 illuminaio_0.8.0 IRanges_2.0.1

[34] iterators_1.0.7 KernSmooth_2.23-14 lattice_0.20-30

[37] limma_3.22.6 locfit_1.5-9.1 MASS_7.3-39

[40] Matrix_1.1-5 matrixStats_0.14.0 mclust_4.4

[43] methylumi_2.12.0 mgcv_1.8-5 minfi_1.12.0

[46] multtest_2.22.0 nleqslv_2.5 nlme_3.1-120

[49] nor1mix_1.2-0 pkgmaker_0.22 plyr_1.8.1

[52] preprocessCore_1.28.0 quadprog_1.5-5 RColorBrewer_1.1-2

[55] Rcpp_0.11.4 RCurl_1.95-4.5 registry_0.2

[58] reshape_0.8.5 rngtools_1.2.4 Rsamtools_1.18.3

[61] RSQLite_1.0.0 rtracklayer_1.26.2 S4Vectors_0.4.0

[64] sendmailR_1.2-1 siggenes_1.40.0 splines_3.1.2

[67] stats4_3.1.2 stringr_0.6.2 survival_2.38-1

[70] tcltk_3.1.2 tools_3.1.2 XML_3.98-1.1

[73] xtable_1.7-4 XVector_0.6.0 zlibbioc_1.12.0

>

ADD COMMENT • link 9.8 years ago Levi Waldron ★ 1.1k

0

Entering edit mode

Thanks! Levi I have just fixed the bug and submit the change to lumi 2.19.1. Before the fix to be released, as a temporary solution, users can first convert the logical values as numeric index using which function and then do subsetting. Pan On Thu, Mar 5, 2015 at 11:37 AM, Levi Waldron [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Levi Waldron <https: support.bioconductor.org="" u="" 3429=""/> wrote Answer: > Removing samples from S4 object (in lumi) > <https: support.bioconductor.org="" p="" 65416="" #65423="">: > > Pan, I think this is a bug in how lumi subsets from logical vectors, not > user error - for example: > > > library(lumi) > > > data(example.lumi) > > > dim(example.lumi) > > Features Samples > > 8000 4 > > > example.lumi[, 1:3] > > Summary of data information: > > Illumina Inc. BeadStudio version 1.4.0.1 > > Normalization = none > > Array Content = 11188230_100CP_MAGE-ML.XML > > Error Model = none > > DateTime = 2/3/2005 3:21 PM > > Local Settings = en-US > > > > > > Major Operation History: > > submitted finished > > 1 2007-04-22 00:08:36 2007-04-22 00:10:36 > > 2 2007-04-22 00:10:36 2007-04-22 00:10:38 > > 3 2007-04-22 00:13:06 2007-04-22 00:13:10 > > 4 2007-04-22 00:59:20 2007-04-22 00:59:36 > > 5 2015-03-05 14:32:23 2015-03-05 14:32:23 > > command lumiVersion > > 1 lumiR("../data/Barnes_gene_profile.txt") 1.1.6 > > 2 lumiQ(x.lumi = x.lumi) 1.1.6 > > 3 addNuId2lumi(x.lumi = x.lumi, lib = "lumiHumanV1") 1.1.6 > > 4 Subsetting 8000 features and 4 samples. 1.1.6 > > 5 Subsetting 4 samples. 2.18.0 > > > > Object Information: > > LumiBatch (storageMode: lockedEnvironment) > > assayData: 8000 features, 3 samples > > element names: beadNum, detection, exprs, se.exprs > > protocolData: none > > phenoData > > sampleNames: A01 A02 B01 > > varLabels: sampleID label > > varMetadata: labelDescription > > featureData > > featureNames: oZsQEQXp9ccVIlwoQo 9qedFRd_5Cul.ueZeQ ... > > 33KnLHy.RFaieogAF4 (8000 total) > > fvarLabels: TargetID > > fvarMetadata: labelDescription > > experimentData: use 'experimentData(object)' > > Annotation: lumiHumanAll.db > > Control Data: Available > > QC information: Please run summary(x, 'QC') for details! > > > example.lumi[, c(T, T, T, F)] > > The sample names in the controlData don't match sampleNames(object). > > Summary of data information: > > Illumina Inc. BeadStudio version 1.4.0.1 > > Normalization = none > > Array Content = 11188230_100CP_MAGE-ML.XML > > Error Model = none > > DateTime = 2/3/2005 3:21 PM > > Local Settings = en-US > > > > > > Major Operation History: > > submitted finished > > 1 2007-04-22 00:08:36 2007-04-22 00:10:36 > > 2 2007-04-22 00:10:36 2007-04-22 00:10:38 > > 3 2007-04-22 00:13:06 2007-04-22 00:13:10 > > 4 2007-04-22 00:59:20 2007-04-22 00:59:36 > > 5 2015-03-05 14:32:23 2015-03-05 14:32:23 > > command lumiVersion > > 1 lumiR("../data/Barnes_gene_profile.txt") 1.1.6 > > 2 lumiQ(x.lumi = x.lumi) 1.1.6 > > 3 addNuId2lumi(x.lumi = x.lumi, lib = "lumiHumanV1") 1.1.6 > > 4 Subsetting 8000 features and 4 samples. 1.1.6 > > 5 Subsetting 4 samples. 2.18.0 > > > > Object Information: > > LumiBatch (storageMode: lockedEnvironment) > > assayData: 8000 features, 3 samples > > element names: beadNum, detection, exprs, se.exprs > > protocolData: none > > phenoData > > sampleNames: A01 A02 B01 > > varLabels: sampleID label > > varMetadata: labelDescription > > featureData > > featureNames: oZsQEQXp9ccVIlwoQo 9qedFRd_5Cul.ueZeQ ... > > 33KnLHy.RFaieogAF4 (8000 total) > > fvarLabels: TargetID > > fvarMetadata: labelDescription > > experimentData: use 'experimentData(object)' > > Annotation: lumiHumanAll.db > > Control Data: Available > > QC information: Please run summary(x, 'QC') for details! > > Warning message: > > In example.lumi[, c(T, T, T, F)] : > > The controlData slot does not match the sampleNames. > > The subsetting did not execute on controlData. > > > > > sessionInfo() > > R version 3.1.2 (2014-10-31) > > Platform: x86_64-pc-linux-gnu (64-bit) > > > > 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] parallel stats graphics grDevices utils datasets methods > > [8] base > > > > other attached packages: > > [1] lumi_2.18.0 Biobase_2.26.0 BiocGenerics_0.12.1 > > > > loaded via a namespace (and not attached): > > [1] affy_1.44.0 affyio_1.34.0 annotate_1.44.0 > > > [4] AnnotationDbi_1.28.1 base64_1.1 base64enc_0.1-2 > > > [7] BatchJobs_1.5 BBmisc_1.9 beanplot_1.2 > > > [10] BiocInstaller_1.16.1 BiocParallel_1.0.3 biomaRt_2.22.0 > > > [13] Biostrings_2.34.1 bitops_1.0-6 brew_1.0-6 > > > [16] BSgenome_1.34.1 bumphunter_1.6.0 checkmate_1.5.1 > > > [19] codetools_0.2-10 colorspace_1.2-5 DBI_0.3.1 > > > [22] digest_0.6.8 doRNG_1.6 fail_1.2 > > > [25] foreach_1.4.2 genefilter_1.48.1 GenomeInfoDb_1.2.4 > > > [28] GenomicAlignments_1.2.2 GenomicFeatures_1.18.3 GenomicRanges_1.18.4 > > > [31] grid_3.1.2 illuminaio_0.8.0 IRanges_2.0.1 > > > [34] iterators_1.0.7 KernSmooth_2.23-14 lattice_0.20-30 > > > [37] limma_3.22.6 locfit_1.5-9.1 MASS_7.3-39 > > > [40] Matrix_1.1-5 matrixStats_0.14.0 mclust_4.4 > > > [43] methylumi_2.12.0 mgcv_1.8-5 minfi_1.12.0 > > > [46] multtest_2.22.0 nleqslv_2.5 nlme_3.1-120 > > > [49] nor1mix_1.2-0 pkgmaker_0.22 plyr_1.8.1 > > > [52] preprocessCore_1.28.0 quadprog_1.5-5 RColorBrewer_1.1-2 > > > [55] Rcpp_0.11.4 RCurl_1.95-4.5 registry_0.2 > > > [58] reshape_0.8.5 rngtools_1.2.4 Rsamtools_1.18.3 > > > [61] RSQLite_1.0.0 rtracklayer_1.26.2 S4Vectors_0.4.0 > > > [64] sendmailR_1.2-1 siggenes_1.40.0 splines_3.1.2 > > > [67] stats4_3.1.2 stringr_0.6.2 survival_2.38-1 > > > [70] tcltk_3.1.2 tools_3.1.2 XML_3.98-1.1 > > > [73] xtable_1.7-4 XVector_0.6.0 zlibbioc_1.12.0 > > > > > > > > ------------------------------ > > You may reply via email or visit > A: Removing samples from S4 object (in lumi) >

ADD REPLY • link 9.8 years ago Pan Du ▴ 80

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Pan Du ▴ 80

@pan-du-4535

Last seen 9.9 years ago

United States

As the error message shows, please check the colnames of controlData. If they are inconsistent with the sampleNames of lumiExpr, just rename them and try again. Pan On Thu, Mar 5, 2015 at 9:54 AM, Chi Hong [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Chi Hong <https: support.bioconductor.org="" u="" 7095=""/> wrote Question: > Removing samples from S4 object (in lumi) > <https: support.bioconductor.org="" p="" 65416=""/>: > > How do I remove (failed) samples from my LumiBatch object? > > > > I've detected outlying samples from the various QC plots generated by > lumiQ (actually, lumiR). I know their sample names. I'd like to remove them > before normalizing the data and subsequent analysis. > > > > I tried something like this: > > sampleNames(lumiExpr) <- pData(lumiExpr)$sampleID > > badsamp = c("5406958048_G","5406958047_I") > > toremove = pData(lumiBatch.object)$sampleID %in% badsamp > > lumiExpr.new = lumiExpr[ , !toremove] > > > > Got this error message: > > The sample names in the controlData don't match sampleNames(object). > Warning message: > In lumiExpr[ , !toremove] : > The controlData slot does not match the sampleNames. > The subsetting did not execute on controlData. > > > > Is there a better way to do this? > > > > > > ------------------------------ > > You may reply via email or visit Removing samples from S4 object (in lumi) >

ADD COMMENT • link 9.8 years ago Pan Du ▴ 80

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Chi Hong • 0

@chi-hong-7095

Last seen 8.9 years ago

United States

Pan,

The colnames of controlData appear to be consistent with sampleNames. See below:

sampleNames(lumiExpr)

[1] "5406958043_A" "5406958043_B" "5406958043_C" "5406958043_D" "5406958043_E"
[6] "5406958043_F" "5406958043_G" "5406958043_H" "5406958043_I" "5406958043_J"
[11] "5406958043_K" "5406958043_L" "5406958047_A" "5406958047_B" "5406958047_C"
[16] "5406958047_D" "5406958047_E" "5406958047_F" "5406958047_G" "5406958047_H"
[21] "5406958047_I" "5406958047_J" "5406958047_K" "5406958047_L" "5406958048_A"
[26] "5406958048_B" "5406958048_C" "5406958048_D" "5406958048_E" "5406958048_F"
[31] "5406958048_G" "5406958048_H" "5406958048_I" "5406958048_J" "5406958048_K"
[36] "5406958048_L"

names(controlData(lumiExpr))
[1] "controlType" "ProbeID" "5406958043_A" "5406958043_B" "5406958043_C"
[6] "5406958043_D" "5406958043_E" "5406958043_F" "5406958043_G" "5406958043_H"
[11] "5406958043_I" "5406958043_J" "5406958043_K" "5406958043_L" "5406958047_A"
[16] "5406958047_B" "5406958047_C" "5406958047_D" "5406958047_E" "5406958047_F"
[21] "5406958047_G" "5406958047_H" "5406958047_I" "5406958047_J" "5406958047_K"
[26] "5406958047_L" "5406958048_A" "5406958048_B" "5406958048_C" "5406958048_D"
[31] "5406958048_E" "5406958048_F" "5406958048_G" "5406958048_H" "5406958048_I"
[36] "5406958048_J" "5406958048_K" "5406958048_L"

table( is.element( names(controlData(lumiExpr)), badsamp ) )

FALSE TRUE
36 2

table( is.element( sampleNames(lumiExpr), badsamp) )

FALSE TRUE
34 2

ADD COMMENT • link 9.8 years ago Chi Hong • 0

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Hi Chi Levi pointed out the problem. And I have fixed the bug in the developing version of lumi. As a temporary solution, please use lumiExpr[, -which(badsamp)] for subsetting. Pan On Thu, Mar 5, 2015 at 1:03 PM, Chi Hong [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Chi Hong <https: support.bioconductor.org="" u="" 7095=""/> wrote Answer: > Removing samples from S4 object (in lumi) > <https: support.bioconductor.org="" p="" 65416="" #65426="">: > > Pan, > > The colnames of controlData appear to be consistent with sampleNames. See > below: > > > > sampleNames(lumiExpr) > > [1] "5406958043_A" "5406958043_B" "5406958043_C" "5406958043_D" " > 5406958043_E" > [6] "5406958043_F" "5406958043_G" "5406958043_H" "5406958043_I" " > 5406958043_J" > [11] "5406958043_K" "5406958043_L" "5406958047_A" "5406958047_B" > "5406958047_C" > [16] "5406958047_D" "5406958047_E" "5406958047_F" "5406958047_G" > "5406958047_H" > [21] "5406958047_I" "5406958047_J" "5406958047_K" "5406958047_L" > "5406958048_A" > [26] "5406958048_B" "5406958048_C" "5406958048_D" "5406958048_E" > "5406958048_F" > [31] "5406958048_G" "5406958048_H" "5406958048_I" "5406958048_J" > "5406958048_K" > [36] "5406958048_L" > > > > names(controlData(lumiExpr)) > [1] "controlType" "ProbeID" "5406958043_A" "5406958043_B" > "5406958043_C" > [6] "5406958043_D" "5406958043_E" "5406958043_F" "5406958043_G" > "5406958043_H" > [11] "5406958043_I" "5406958043_J" "5406958043_K" "5406958043_L" > "5406958047_A" > [16] "5406958047_B" "5406958047_C" "5406958047_D" "5406958047_E" > "5406958047_F" > [21] "5406958047_G" "5406958047_H" "5406958047_I" "5406958047_J" > "5406958047_K" > [26] "5406958047_L" "5406958048_A" "5406958048_B" "5406958048_C" > "5406958048_D" > [31] "5406958048_E" "5406958048_F" "5406958048_G" "5406958048_H" > "5406958048_I" > [36] "5406958048_J" "5406958048_K" "5406958048_L" > > > > table( is.element( names(controlData(lumiExpr)), badsamp ) ) > > FALSE TRUE > 36 2 > > > > table( is.element( sampleNames(lumiExpr), badsamp) ) > > FALSE TRUE > 34 2 > > > > > > ------------------------------ > > You may reply via email or visit > A: Removing samples from S4 object (in lumi) >

ADD REPLY • link 9.8 years ago Pan Du ▴ 80

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Great! Thanks, Pan! On Thu, Mar 5, 2015 at 4:11 PM, Pan Du [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Pan Du <https: support.bioconductor.org="" u="" 4535=""/> wrote Comment: > Removing samples from S4 object (in lumi) > <https: support.bioconductor.org="" p="" 65416="" #65427="">: > > Hi Chi Levi pointed out the problem. And I have fixed the bug in the > developing version of lumi. As a temporary solution, please use lumiExpr[, > -which(badsamp)] for subsetting. Pan On Thu, Mar 5, 2015 at 1:03 PM, Chi > Hong [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you > are following on support.bioconductor.org > > User Chi Hong <https:> support.bioconductor.org="" u="" 7095=""/> wrote Answer: > Removing > samples from S4 object (in lumi) > <https: support.bioconductor.org=""> p="" 65416="" #65426="">: > > Pan, > > The colnames of controlData appear > to be consistent with sampleNames. See > below: > > > > > sampleNames(lumiExpr) > > [1] "5406958043_A" "5406958043_B" "5406958043_C" > "5406958043_D" " > 5406958043_E" > [6] "5406958043_F" "5406958043_G" " > 5406958043_H" "5406958043_I" " > 5406958043_J" > [11] "5406958043_K" " > 5406958043_L" "5406958047_A" "5406958047_B" > "5406958047_C" > [16] > "5406958047_D" "5406958047_E" "5406958047_F" "5406958047_G" > > "5406958047_H" > [21] "5406958047_I" "5406958047_J" "5406958047_K" > "5406958047_L" > "5406958048_A" > [26] "5406958048_B" "5406958048_C" > "5406958048_D" "5406958048_E" > "5406958048_F" > [31] "5406958048_G" > "5406958048_H" "5406958048_I" "5406958048_J" > "5406958048_K" > [36] > "5406958048_L" > > > > names(controlData(lumiExpr)) > [1] "controlType" > "ProbeID" "5406958043_A" "5406958043_B" > "5406958043_C" > [6] > "5406958043_D" "5406958043_E" "5406958043_F" "5406958043_G" > > "5406958043_H" > [11] "5406958043_I" "5406958043_J" "5406958043_K" > "5406958043_L" > "5406958047_A" > [16] "5406958047_B" "5406958047_C" > "5406958047_D" "5406958047_E" > "5406958047_F" > [21] "5406958047_G" > "5406958047_H" "5406958047_I" "5406958047_J" > "5406958047_K" > [26] > "5406958047_L" "5406958048_A" "5406958048_B" "5406958048_C" > > "5406958048_D" > [31] "5406958048_E" "5406958048_F" "5406958048_G" > "5406958048_H" > "5406958048_I" > [36] "5406958048_J" "5406958048_K" > "5406958048_L" > > > > table( is.element( names(controlData(lumiExpr)), > badsamp ) ) > > FALSE TRUE > 36 2 > > > > table( is.element( > sampleNames(lumiExpr), badsamp) ) > > FALSE TRUE > 34 2 > > > > > > > ------------------------------ > > You may reply via email or visit > A: > Removing samples from S4 object (in lumi) > <https: support.bioconductor.org="" p="" 65416="" #65426=""> > > > ------------------------------ > > You may reply via email or visit > C: Removing samples from S4 object (in lumi) >

ADD REPLY • link 9.8 years ago Chi Hong • 0

score 1 · Accepted Answer · 2015-03-05

Summarizing a side-conversation:

Levi was correct. The bug is now fixed and will be a part of lumi 2.19.1.

Here's the temporary solution to remove 2 samples ('badsamp') (Thanks, Pan!):

sampleNames(lumiExpr) = pData(lumiExpr)$sampleID
badsamp = c("5406958048_G","5406958047_I")
toremove = pData(lumiExpr)$sampleID %in% badsamp
lumiExpr.new= lumiExpr[,-which(toremove)]

dim(lumiExpr.new)
Features Samples
47231 34

dim(lumiExpr)
Features Samples
47231 36