Hi Andreas,

Thanks for replying. If I can fix the problem with virtualArrays I will 
cite for sure. Here is the information for expression matrices from both 
datasets:

>head(exprs(AF.mydata))
   10.5A.CEL 10.5B.CEL 10.5C.CEL 11.5A.CEL 11.5B.CEL 11.5C.CEL 12.5A.CEL 12.5B.CEL 12.5C.CEL E17.5A.CEL
1       105       128       104       114       159       227       129       158       182         74
2     14320     19105     11777     14959     19861     17099     14849     21567     20675       9377
3       127       187       115       187       163       455       165       269       244         79
4     14927     19889     11911     15203     19997     18227     15369     22589     20806       9655
5        92       150        88        73       103       259        89       113       234         83
6       110        98       113       139       144       161        98       132       159         61
   E17.5B.CEL E17.5C.CEL E17.5D.CEL E17.5E.CEL E19.5A_.CEL E19.5B.CEL E19.5C.CEL P0A.CEL P0B.CEL P0C.CEL
1         78         68         72         60         134        223        120      75      69      65
2       9395       9786      10567      10824       10034       8349      10384    7492    6381    8700
3        120        117        140        127         205        231        248      96      66      83
4       9597       9972      10903      11056       10381       8328      10232    7591    6465    8420
5         61         76         63         50         136        176        102      73      60      84
6         74         58         65         74         130        172        127      91      49      63
   P0D.CEL P0E.CEL P28A.CEL P28B.CEL P28C.CEL P2A.CEL P2B.CEL P2C.CEL WB_AF_A.CEL WB_AF_B.CEL WB_AF_C.CEL
1      68      59       71       77       56     166     168     185         172         158          96
2    7272    9501       46       49       41   14202   13199   13267       18186       14627       13158
3      85     160       78       65       58     210     214     196         189         158         151
4    7524    9664       57       55       46   14759   13533   14263       18918       15468       13308
5      64      72       41       46       44     144     192     138         145         194         106
6      65      68       88       76       58     156     149     177         119         145         109
>head(exprs(IL.mydataA))
                          P4_C1       P4_C2       P4_C3          T1          T2           T3      P30_C1
T.kvUVfFyruaCeqZVs   -4.704992   -5.008878    4.013575   -7.155298   -1.018183   -0.5739443   -1.218571
Q96MoiqM_z49FU37tE   -5.498747    4.351016    7.339304    6.459189    1.064443    1.2691800   -7.323681
WpaZ9x9f_hAnoR.VBE 2483.110000 2872.099000 2461.915000 2399.139000 3167.442000 2507.4980000 3831.747000
ZhdXp75JftSF3iWLF4  467.483700  564.803300  502.616200  429.565400  848.511400  473.4642000  690.122100
QoJVn30kwRGJ3SN9Q4    5.977465    8.649684   -6.068388   -2.379038   -3.892618   -0.8772737   -1.730694
xnx7ijE2CcOSlY55eA  525.841000  588.122100  577.280500  493.595600  540.728800  559.2224000  713.712900
                          P30_C2      P30_C3           51           55           56
T.kvUVfFyruaCeqZVs    1.4039610   -7.777119   -8.5276410   -9.3387030   -0.5762033
Q96MoiqM_z49FU37tE   -0.2668989    4.637646   -0.4015962   -0.8310394    1.8641310
WpaZ9x9f_hAnoR.VBE 3169.7620000 3210.845000 3391.7170000 3615.6720000 2988.9270000
ZhdXp75JftSF3iWLF4  577.8732000  580.200300  582.7916000  654.7377000  616.9252000
QoJVn30kwRGJ3SN9Q4   -3.8180120    7.699070   -5.1443480    2.5087130   -2.0737350
xnx7ijE2CcOSlY55eA  335.6019000  463.035400  657.2077000  717.1554000  522.6875000



Waiting for your reply

Best

AK





On 06-Jun-13 3:38 AM, Andreas Heider wrote:
> Dear Atul,
> first of all: Thanks for using my package!
> I think the error you get directly relates to your Illumina Dataset. 
> Can you send me a "head()" of the expression matrices of both 
> datasets? Then we will see the problem there. There are several way to 
> load in Illumina datasets, and we need to use the right one.
>
> Please, do not hessitate to contact me again. And please cite my work in:
> http://www.biomedcentral.com/1471-2105/14/75
>
> Yours sincerely,
> Andreas Heider
>
>
> 2013/5/31 Atul Kakrana <atulkakrana@outlook.com 
> <mailto:atulkakrana@outlook.com>>
>
>     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 <http://AF.eset.BG> <- bg.correct.rma(AF.mydata)
>     IL.eset.BG <http://IL.eset.BG> <- lumiB(IL.mydata, method =
>     c('bgAdjust.affy'))
>
>     virtArrays.EB <-
>     virtualArrayExpressionSets(all_expression_sets=c('AF.eset.BG
>     <http://AF.eset.BG>','IL.eset.BG <http://IL.eset.BG>'),identifier
>     = 'SYMBOL')
>
>
>     SCREEN OUTPUT/ERROR:
>
>     >virtArrays.EB <- virtualArrayExpressionSets(all_expression_sets=c('AF.eset.BG  <http://AF.eset.BG>','IL.eset.BG  <http://IL.eset.BG>'),identifier = 'SYMBOL')
>
>     Now preprocessing raw data ofAF.eset.BG  <http://AF.eset.BG>  : Loading annotations...
>
>     Now preprocessing raw data ofAF.eset.BG  <http://AF.eset.BG>  : Collapsing expression values to their  median ...
>     Using identifier as id variables
>
>     Now preprocessing raw data ofAF.eset.BG  <http://AF.eset.BG>  : Annotating expression values with  SYMBOL ...
>
>     Size of expression matrix ofAF.eset.BG  <http://AF.eset.BG>  : 22051 rows and 31 columns
>
>     Now preprocessing raw data ofIL.eset.BG  <http://IL.eset.BG>  : Loading annotations...
>
>     Now preprocessing raw data ofIL.eset.BG  <http://IL.eset.BG>  : Collapsing expression values to their  median ...
>     Using identifier as id variables
>
>     Now preprocessing raw data ofIL.eset.BG  <http://IL.eset.BG>  : Annotating expression values with  SYMBOL ...
>
>     Size of expression matrix ofIL.eset.BG  <http://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 ofAF.eset.BG  <http://AF.eset.BG>  ...
>
>     Now setting up pData ofIL.eset.BG  <http://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.
>
>
>
>


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