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Question: virtualArray package - Error while combing data sets
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gravatar for Bade
4.5 years ago by
Bade310
Delaware
Bade310 wrote:
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. > > > > [[alternative HTML version deleted]]
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