virtualArray package - Error while combing data sets
0
0
Entering edit mode
Bade ▴ 310
@bade-5877
Last seen 3.9 years ago
Delaware
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]]
Preprocessing virtualArray Preprocessing virtualArray • 1.3k views
ADD COMMENT

Login before adding your answer.

Traffic: 699 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6