[BioC] diagnosing problems with processing microarray data using lumi package

[Juliet Hannah]

List,

I have illumina microarray data and I'm trying to use the lumi package
to process it. I am running into some difficulties, and I am looking
for suggestions on how to diagnose what is going wrong.

# read in expression data

fileName <- "samples.txt"
myData  <- lumiR(fileName)

Duplicated IDs found and were merged!
Perform Quality Control assessment of the LumiBatch object ...
Warning messages:
1: In lumiR(fileName) :
  The data file may not be in the Illumia BeadStudio or GenomeStudio
output format!

2: In matrix(as.double(exprs), nrow = nrow(allData)) :
  NAs introduced by coercion
3: In matrix(as.double(se.exprs), nrow = nrow(allData)) :
  NAs introduced by coercion
4: In matrix(as.double(detection), nrow = nrow(allData)) :
  NAs introduced by coercion
5: In matrix(as.double(beadNum), nrow = nrow(allData)) :
  NAs introduced by coercion

# the names for the controls are not compatible with a data.frame so I
had to change these.

 newNames <- paste("X",sampleNames(myData),sep="")
 newNames <- sub("-",".",newNames)

 sampleNames(myData) <- newNames

# read in controls

 fileName <- "controls.txt"
 controls  <- lumiR(fileName)

Annotation columns are not available in the data.
Duplicated IDs found and were merged!
Perform Quality Control assessment of the LumiBatch object ...
Warning message:
In lumiR(fileName) :
  The data file may not be in the Illumia BeadStudio or GenomeStudio
output format!

# convert to data frame so I can add it to controlData slot

 controls <- exprs(controls)
 colnames(controls) <- paste("X",colnames(controls),sep="")
 controls <- data.frame(controls)

 myData at controlData <- controls
 lnormdata <- lumiB(myData,method='bgAdjust')
Perform bgAdjust background correction ...

# attempting VST, but having problems

tryVST  <- lumiT(lnormdata)
Perform vst transformation ...
2011-11-17 16:34:50 , processing array  1
2011-11-17 16:34:50 , processing array  2
2011-11-17 16:34:50 , processing array  3
2011-11-17 16:34:50 , processing array  4
2011-11-17 16:34:51 , processing array  5
2011-11-17 16:34:51 , processing array  6
2011-11-17 16:34:51 , processing array  7
2011-11-17 16:34:51 , processing array  8
2011-11-17 16:34:51 , processing array  9
2011-11-17 16:34:51 , processing array  10
2011-11-17 16:34:51 , processing array  11
2011-11-17 16:34:51 , processing array  12
Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) :
  0 (non-NA) cases
In addition: Warning messages:
1: In lumiT(lnormdata) :
  Too few probes are detectable based on detection p-values!

                                                Iteration method will
be used for VST.
2: In lumiT(lnormdata) :
  Too few probes are detectable based on detection p-values!

                                                Iteration method will
be used for VST.
3: In lumiT(lnormdata) :
  Too few probes are detectable based on detection p-values!

                                                Iteration method will
be used for VST.


Can anyone suggest how to diagnose what is going wrong? Thanks for your help.



In case it is useful at all, the beginning of the file looks like.

[Sample Probe Profile]	
PROBE_ID	SYMBOL	262-00715.AVG_Signal	262-00715.NARRAYS	262-00715.ARRAY_STDEV	262-00715.BEAD_STDERR	262-00715.Avg_NBEADS

> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-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=C                 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] lumi_2.6.0      nleqslv_1.9.0   methylumi_2.0.1 Biobase_2.14.0

loaded via a namespace (and not attached):
 [1] affy_1.32.0           affyio_1.22.0         annotate_1.32.0
 [4] AnnotationDbi_1.16.2  BiocInstaller_1.2.1   DBI_0.2-5
 [7] grid_2.14.0           hdrcde_2.15           IRanges_1.12.1
[10] KernSmooth_2.23-7     lattice_0.20-0        MASS_7.3-16
[13] Matrix_1.0-1          mgcv_1.7-11           nlme_3.1-102
[16] preprocessCore_1.16.0 RSQLite_0.10.0        xtable_1.6-0
[19] zlibbioc_1.0.0