Hi Andreas (and everybody),

I am using virtualArray package to combine Illumina and Affymetrix 
micro-array datasets. As mentioned in the virtualArray manual and 
publication I prepared 'ExpressionSet' from both affymetrix and Illumina 
datasets. But while compiling a 'virtualarray' I get an error.

MINIMAL CODE:

IL.mydata <- lumiR.batch(filelist)
AF.mydata <- ReadAffy()

AF.eset.BG <- bg.correct.rma(AF.mydata)
IL.eset.BG <- lumiB(IL.mydata, method = c('bgAdjust.affy'))

virtArrays.EB <- 
virtualArrayExpressionSets(all_expression_sets=c('AF.eset.BG','IL.eset.BG'),identifier 
= 'SYMBOL')


SCREEN OUTPUT/ERROR:

>virtArrays.EB <- virtualArrayExpressionSets(all_expression_sets=c('AF.eset.BG','IL.eset.BG'),identifier = 'SYMBOL')

Now preprocessing raw data of  AF.eset.BG : Loading annotations...

Now preprocessing raw data of  AF.eset.BG : Collapsing expression values to their  median ...
Using identifier as id variables

Now preprocessing raw data of  AF.eset.BG : Annotating expression values with  SYMBOL ...

Size of expression matrix of AF.eset.BG : 22051 rows and 31 columns

Now preprocessing raw data of  IL.eset.BG : Loading annotations...

Now preprocessing raw data of  IL.eset.BG : Collapsing expression values to their  median ...
Using identifier as id variables

Now preprocessing raw data of  IL.eset.BG : Annotating expression values with  SYMBOL ...

Size of expression matrix of IL.eset.BG : 19443 rows and 6 columns

Matching and merging all data sets. This could take some time...

Size of expression matrix of whole dataset: 16536 rows and 37 columns

Now combining pData of all data sets...

Now setting up pData of  AF.eset.BG ...

Now setting up pData of  IL.eset.BG ...

The file 'sample_info.txt' has been written to your current working directory. Please modify it appropriately!

Using only 'Batch' column as information for batch effect removal.
Reading Sample Information File
Reading Expression Data File
Found 2 batches
Found 0 covariate(s)
Found 544800 Missing Data Values
Standardizing Data across genes
Error in solve.default(t(des) %*% des) :
   Lapack routine dgesv: system is exactly singular: U[1,1] = 0


I am not being able to understand the reason behind the error and would 
really appreciate help on this. I have come across few potential bugs in 
virtualArrays pack too which I will post once done with this part.

Session Info:

>sessionInfo()
R version 2.15.3 (2013-03-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
  [1] lumiMouseAll.db_1.18.0 lumi_2.10.0            nleqslv_2.0            mouse4302.db_2.8.1
  [5] org.Mm.eg.db_2.8.0     RSQLite_0.11.4         DBI_0.2-7              AnnotationDbi_1.20.7
  [9] Biobase_2.18.0         BiocGenerics_0.4.0     virtualArray_1.2.1     preprocessCore_1.20.0
[13] plyr_1.8

loaded via a namespace (and not attached):
  [1] affy_1.36.1         affyio_1.26.0       affyPLM_1.34.0      annotate_1.36.0
  [5] BiocInstaller_1.8.3 Biostrings_2.26.3   colorspace_1.2-2    gcrma_2.30.0
  [9] GEOquery_2.24.1     grid_2.15.3         IRanges_1.16.6      KernSmooth_2.23-10
[13] lattice_0.20-15     MASS_7.3-23         Matrix_1.0-12       methylumi_2.4.0
[17] mgcv_1.7-23         nlme_3.1-108        parallel_2.15.3     RCurl_1.95-4.1
[21] reshape2_1.2.2      splines_2.15.3      stats4_2.15.3       stringr_0.6.2
[25] tools_2.15.3        XML_3.96-1.1        xtable_1.7-1        zlibbioc_1.4.0


Thanks

A.




	[[alternative HTML version deleted]]

