[BioC] Beadarray - problem with BSData object created using 'summarize'

[Kasia Stepien]

Hello!

I am using beadarray v 2.0.2 to analyze beadlevel data for Illumina
RatRef-12 whole genome gene expression arrays (I have 8 chips, with 12
samples each, for a total of 96 arrays).

When trying to create a bead summary object using "summarize", the
section names from the BLData object appear to be recycled (eg.
"5398636011_A", "5398636011_A.1", rather than "5398636011_A",
"5398636011_B", etc). At first I thought the arrays themselves were
being used reused, but the similarly named objects do not appear to be
identical (see below).

What could the reason be for this? Is there some argument for
summarize that I can use to get around this problem?

This is what it looks like for 2 chips, with 12 samples each:

> BLData1 = readIllumina(dir="/home/kasia/kasiadata/5398636011filtered/", useImages=FALSE, illuminaAnnotation="Ratv1")
Processing section 5398636011_A
Processing section 5398636011_B
Processing section 5398636011_C
Processing section 5398636011_D
Processing section 5398636011_E
Processing section 5398636011_F
Processing section 5398636011_G
Processing section 5398636011_H
Processing section 5398636011_I
Processing section 5398636011_J
Processing section 5398636011_K
Processing section 5398636011_L
> BLData2 = readIllumina(dir="/home/kasia/kasiadata/5398636033filtered/", useImages=FALSE, illuminaAnnotation="Ratv1")
Processing section 5398636033_A
Processing section 5398636033_B
Processing section 5398636033_C
Processing section 5398636033_D
Processing section 5398636033_E
Processing section 5398636033_F
Processing section 5398636033_G
Processing section 5398636033_H
Processing section 5398636033_I
Processing section 5398636033_J
Processing section 5398636033_K
Processing section 5398636033_L
> BLDataCombo = combine(BLData1, BLData2)
> is(BLDataCombo)
[1] "beadLevelData"
> sectionNames(BLDataCombo)
 [1] "5398636011_A" "5398636011_B" "5398636011_C" "5398636011_D" "5398636011_E"
 [6] "5398636011_F" "5398636011_G" "5398636011_H" "5398636011_I" "5398636011_J"
[11] "5398636011_K" "5398636011_L" "5398636033_A" "5398636033_B" "5398636033_C"
[16] "5398636033_D" "5398636033_E" "5398636033_F" "5398636033_G" "5398636033_H"
[21] "5398636033_I" "5398636033_J" "5398636033_K" "5398636033_L"

> myMean = function(x) mean(x, na.rm = TRUE)
> mySd = function(x) sd(x, na.rm = TRUE)
> greenChannel = new("illuminaChannel", logGreenChannelTransform, illuminaOutlierMethod, myMean, mySd, "G")
> BSData <- summarize(BLDataCombo, list(greenChannel))
> str(exprs(BSData))
 num [1:23350, 1:24] 9.92 7.42 7.43 7.5 12.34 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:23350] "ILMN_2039396" "ILMN_2040732" "ILMN_2039699"
"ILMN_2038916" ...
  ..$ : chr [1:24] "5398636011_A" "5398636033_B" "5398636011_C"
"5398636033_D" ...

> colnames(exprs(BSData))
 [1] "5398636011_A"   "5398636033_B"   "5398636011_C"   "5398636033_D"
 [5] "5398636011_E"   "5398636033_F"   "5398636011_G"   "5398636033_H"
 [9] "5398636011_I"   "5398636033_J"   "5398636011_K"   "5398636033_L"
[13] "5398636011_A.1" "5398636033_B.1" "5398636011_C.1" "5398636033_D.1"
[17] "5398636011_E.1" "5398636033_F.1" "5398636011_G.1" "5398636033_H.1"
[21] "5398636011_I.1" "5398636033_J.1" "5398636011_K.1" "5398636033_L.1"

> identical(exprs(BSData)[,1],exprs(BSData)[,13])
[1] FALSE

> head(cbind(exprs(BSData)[,1],exprs(BSData)[,13]))
                  [,1]      [,2]
ILMN_2039396  9.917607  9.817626
ILMN_2040732  7.415167  7.436922
ILMN_2039699  7.432883  7.423043
ILMN_2038916  7.504111  7.619327
ILMN_1374916 12.342863 13.377692
ILMN_1353986  7.210915  7.211393


> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-redhat-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=C              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] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] illuminaRatv1BeadID.db_1.8.0 org.Rn.eg.db_2.4.6
[3] RSQLite_0.9-2                DBI_0.2-5
[5] AnnotationDbi_1.12.0         beadarray_2.0.2
[7] Biobase_2.8.0

loaded via a namespace (and not attached):
[1] KernSmooth_2.23-4 limma_3.4.5       tools_2.12.1



Thank you!
Kasia

-- 
Kasia Stepien, M.Sc. Candidate
Department of Medical Genetics
University of British Columbia