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?

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

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        

> 

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