Pan Du | 28 Jun 08:38 2013
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Re: lumiR returns ExpressionSet object instead of LumiBatch

Hi Liu X

This is because your data does not include the bead standard error
information for the probes (columns are named like "BEAD_STDERR"), which is
required for LumiBatch class. If this information is missing, the lumiR
will just output an ExpressionSet object. Please check the help of lumiR
and the lumi.pdf vignette for more details.

Pan

On Thu, Jun 27, 2013 at 7:30 PM, Liu X [guest] <guest@...>wrote:

>
> Hello,
>
> It is my first time trying to use lumi package to analyze beadchip data by
> following the instruction in vignettes (dated 2013/4/4). However I run into
> problems. Trying to use lumiR to read in a beadstudio export file with
> following commands:
>
> library(lumi)
> library(illumi
> sampfile <- 'path/to/sample_probe_profile.txt'
> lumi.sample<-lumiR(sampfile, lib.mapping="lumiMouseIDMapping",
> annotationColumn = c('PROBE_ID', 'SYMBOL', 'ILMN_GENE', 'CHROMOSOME',
> 'DEFINITION', 'SYNONYMS') )
>
> It runs without error, but class(lumi.sample) tells me that it is an
> ExpressionSet object not LumiBatch. And of course I cannt apply lumi
> methods to analyze it.
>
> What wrong with my steps?
>
> Thanks!
>
> Here is the first 15 lines of the probe_profile file:
> PROBE_ID        SYMBOL  NT1.AVG_Signal  NT1.Detection Pval
>  NT2.AVG_Signal  NT2.Detection Pval      NT3.AVG_Signal  NT3.Detection Pval
>      R1.AVG_Signal   R1.Detection PvalR2.AVG_Signal   R2.Detection Pval
>   R3.AVG_Signal   R3.Detection Pval       M1_2.AVG_Signal M1_2.Detection
> Pval     HG1_2.AVG_Signal        HG1_2.Detection Pval    M1.AVG_Signal
>  M1.Detection Pval       M2.AVG_Signal   M2.Detection Pval
> M3.AVG_Signal   M3.Detection Pval       HG1.AVG_Signal  HG1.Detection Pval
>      HG2.AVG_Signal  HG2.Detection Pval       HG3.AVG_Signal  HG3.Detection
> Pval      NT1_2.AVG_Signal        NT1_2.Detection Pval    R1_2.AVG_Signal
> R1_2.Detection Pval     SEARCH_KEY      ILMN_GENE       CHROMOSOME
> DEFINITION      SYNONYMS
> ILMN_2896528    0610006I08Rik   2607.672        0.00    2527.176
>  0.00    2774.688        0.00    1997.495        0.00    2124.155
>  0.00    2544.899        0.00    3062.838 0.00    3381.947        0.00
>  2546.513        0.00    3017.973        0.00    2987.024        0.00
>  3376.653        0.00    2492.156        0.00    3577.373        0.00
> 2659.114        0.00    2353.836        0.00    ILMN_220369
> 0610006I08RIK   19      Mus musculus RIKEN cDNA 0610006I08 gene
> (0610006I08Rik), mRNA.
> ILMN_2721178    0610006I08Rik   335.6214        0.00    309.3783
>  0.00    311.5328        0.00    255.2664        0.00    253.7414
>  0.00    304.8765        0.00    363.3045 0.00    416.1963        0.00
>  285.1985        0.00    417.5847        0.00    356.8044        0.00
>  371.7544        0.00    308.4683        0.00    533.7448        0.00
> 304.7859        0.00    259.3861        0.00    ILMN_220369
> 0610006I08RIK   19      Mus musculus RIKEN cDNA 0610006I08 gene
> (0610006I08Rik), mRNA.
> ILMN_3033922    0610007C21Rik   1435.676        0.00    1407.494
>  0.00    1813.653        0.00    1138.474        0.00    1199.863
>  0.00    1369.412        0.00    1186.747 0.00    1436.43 0.00    1138.299
>        0.00    1344.861        0.00    1320.021        0.00    1378.295
>    0.00    1026.762        0.00    1909.174        0.00    1361.688 0.00
>  1232.837        0.00    ILMN_244468     0610007C21RIK   5       Mus
> musculus RIKEN cDNA 0610007C21 gene (0610007C21Rik), transcript variant 1,
> mRNA.    AI316792; HSPC013; Apr3; p18
> ILMN_3092673    0610007C21Rik   11323.47        0.00    9251.417
>  0.00    11511.11        0.00    9007.652        0.00    8195.785
>  0.00    9388.674        0.00    9282.038 0.00    9625.286        0.00
>  8375.805        0.00    9982.474        0.00    9821.961        0.00
>  9076.46 0.00    7963.4  0.00    9219.595        0.00    10254.2 0.00
> 9168.383        0.00    ILMN_229637     0610007C21RIK   5       Mus
> musculus RIKEN cDNA 0610007C21 gene (0610007C21Rik), transcript variant 2,
> mRNA.    AI316792; HSPC013; Apr3; p18
> ILMN_2816356    0610007P08Rik   25.62827        0.09398496      45.53978
>      0.02380952      0.5504513       0.3784461       23.20286
>  0.0989975       7.337133        0.2568922        16.80947        0.1566416
>       18.40724        0.1478697       31.25397        0.0764411
> 0.1861096       0.3759398       10.07403        0.2255639       16.067
> 0.1503759       21.37516        0.1027569       6.433805        0.2393484
>     24.07508        0.08646616      24.31498        0.08646616
>  26.45578        0.08270676       ILMN_196322     0610007P08RIK   13
>  Mus musculus RIKEN cDNA 0610007P08 gene (0610007P08Rik), transcript
> variant 2, mRNA.    RAD26L; 1700019D06Rik
> ILMN_2808939    0610007P14Rik   712.1257        0.00    624.3039
>  0.00    779.4008        0.00    695.1705        0.00    671.4506
>  0.00    787.93  0.00    756.97860.00     476.1805        0.00    574.3113
>        0.00    746.5471        0.00    743.4769        0.00    422.7865
>    0.00    376.804 0.00    620.1172        0.00    607.81810.00
> 753.4628        0.00    ILMN_239772     0610007P14RIK   12      Mus
> musculus RIKEN cDNA 0610007P14 gene (0610007P14Rik), mRNA.  AU019315;
> C77855; 1190004E09Rik; ORF11
> ILMN_2634564    0610007P22Rik   595.3325        0.00    451.3885
>  0.00    580.5104        0.00    371.2965        0.00    492.7807
>  0.00    479.4933        0.00    549.2484 0.00    494.6838        0.00
>  401.5907        0.00    437.3422        0.00    539.7564        0.00
>  471.3762        0.00    331.5264        0.00    516.2159        0.00
> 535.5032        0.00    477.19  0.00    ILMN_213192     0610007P22RIK   17
>      Mus musculus RIKEN cDNA 0610007P22 gene (0610007P22Rik), mRNA.
>  AL022759; MGC113771; 1110014B11Rik
> ILMN_2737647    0610008C08Rik   -0.5213413      0.4085213       7.743881
>      0.254386        4.068563        0.3157895       6.312949
>  0.2593985       7.170675        0.2606516        10.64135        0.2155388
>       25.66834        0.0877193       7.385303        0.2593985
> -5.414614       0.5413534       0.8812458       0.3822055       14.31114
> 0.1716792       -3.741079       0.5012531       13.13283        0.1390978
>     -2.912084       0.4724311       -13.54885       0.8233083
> -6.836047       0.6052632ILMN_221600     0610008C08RIK   X       Mus
> musculus RIKEN cDNA 0610008C08 gene (0610008C08Rik), mRNA.  RP23-272D10.2;
> MGC130105; MGC130106; 1110019O03Rik
> ILMN_2734484    0610009B22Rik   1660.084        0.00    1600.733
>  0.00    1853.014        0.00    1533.854        0.00    1641.063
>  0.00    1688.237        0.00    1758.677 0.00    1718.719        0.00
>  1528.311        0.00    1867.37 0.00    1768.41 0.00    1607.629
>  0.00    1211.871        0.00    1692.573        0.00    1825.8470.00
> 1744.845        0.00    ILMN_221361     0610009B22RIK   11      Mus
> musculus RIKEN cDNA 0610009B22 gene (0610009B22Rik), mRNA.  RP23-79E13.7
> ILMN_2952292    0610009D07Rik   161.6432        0.00    150.4215
>  0.00    216.1236        0.00    169.6933        0.00    141.3559
>  0.00    208.3837        0.00    183.1769 0.00    113.102 0.00    145.3057
>        0.00    174.5983        0.00    196.8766        0.00    98.69936
>    0.00    85.1308 0.00    135.3256        0.00    207.43860.00
> 199.6864        0.00    ILMN_218698     0610009D07RIK   12      Mus
> musculus RIKEN cDNA 0610009D07 gene (0610009D07Rik), mRNA.  6030419K15Rik;
> AV001342; Sf3b14
> ILMN_2699078    0610009D07Rik   -13.64666       0.7719298       -17.76805
>       0.9285714       -13.25819       0.7243108       -7.510522
> 0.6127819       -21.9306        0.9699248        -17.45373       0.8696742
>       -19.45185       0.9360902       -9.678173       0.6303258
> -5.608812       0.5501253       -10.17932       0.6729323       -17.24747
>      0.8746867       -16.90044       0.9172933       -8.415766
> 0.7230576       -11.58076       0.7481203       -20.62218       0.9761904
>     -9.215716       0.6654136        ILMN_218698     0610009D07RIK   12
>  Mus musculus RIKEN cDNA 0610009D07 gene (0610009D07Rik), mRNA.
>  6030419K15Rik; AV001342; Sf3b14
> ILMN_1213681    0610009O20Rik   177.286 0.00    146.7101        0.00
>  148.6533        0.00    136.2325        0.00    194.6553        0.00
>  193.7644        0.00    165.37730.00     167.7943        0.00    163.8992
>        0.00    221.8292        0.00    197.5723        0.00    203.4886
>    0.00    139.8207        0.00    300.4458        0.00    163.7285 0.00
>  179.5151        0.00    ILMN_220613     0610009O20RIK   18      Mus
> musculus RIKEN cDNA 0610009O20 gene (0610009O20Rik), mRNA.  2700004E22Rik
> ILMN_2735413    0610010D20Rik   7.146307        0.2706767       7.9561
>  0.2468672       24.70525        0.1102757       5.685019        0.2719298
>       10.20794        0.2155388-4.846704       0.5213032       -3.845815
>     0.4874687       -6.052074       0.5238096       -6.612185
> 0.5827067       1.393941        0.3759398       -11.49365       0.735589
> 1.478938        0.3558897       5.659925        0.2506266       9.050623
>      0.226817        -2.104225       0.4398496       -15.24391
> 0.8558897       ILMN_221425      0610010D20RIK   19      Mus musculus RIKEN
> cDNA 0610010D20 gene (0610010D20Rik), mRNA.
> ILMN_2735415    0610010D20Rik   -11.26077       0.7067669       -0.4047703
>      0.4035088       6.900579        0.2807018       0.7097692
> 0.3834586       -7.749537       0.6215539        -16.24752       0.8446115
>       17.96398        0.1503759       5.702412        0.2819549
> 5.526793        0.2869674       11.87896        0.2017544       1.067933
> 0.3734336       -10.01922       0.7205514       -0.05420115     0.4110276
>     -3.374624       0.4837093       12.72869        0.1691729
> -8.716571       0.6453634ILMN_221425     0610010D20RIK   19      Mus
> musculus RIKEN cDNA 0610010D20 gene (0610010D20Rik), mRNA.
>
>
>
>
>  -- output of sessionInfo():
>
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] grid      parallel  stats     graphics  grDevices utils     datasets
>  methods   base
>
> other attached packages:
>  [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2  GenomicFeatures_1.12.2
>  [3] lumiMouseIDMapping_1.10.0                lumi_2.12.0
>  [5] BSgenome.Scerevisiae.UCSC.sacCer1_1.3.17 sagenhaft_1.30.0
>  [7] SparseM_0.99                             edgeR_3.2.3
>  [9] limma_3.16.5                             hexbin_1.26.2
> [11] BSgenome_1.28.0                          ShortRead_1.18.0
> [13] latticeExtra_0.6-24                      RColorBrewer_1.0-5
> [15] lattice_0.20-15                          Rsamtools_1.12.3
> [17] Biostrings_2.28.0                        rtracklayer_1.20.2
> [19] GenomicRanges_1.12.4                     IRanges_1.18.1
> [21] gaschYHS_1.0.11                          org.Hs.eg.db_2.9.0
> [23] org.Sc.sgd.db_2.9.1                      BiocInstaller_1.10.2
> [25] GO.db_2.9.0                              RSQLite_0.11.4
> [27] DBI_0.2-7                                AnnotationDbi_1.22.6
> [29] Biobase_2.20.0                           BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
>  [1] affy_1.38.1           affyio_1.28.0         annotate_1.38.0
> beanplot_1.1
>  [5] biomaRt_2.16.0        bitops_1.0-5          colorspace_1.2-2
>  hwriter_1.3
>  [9] illuminaio_0.2.0      KernSmooth_2.23-10    MASS_7.3-26
> Matrix_1.0-12
> [13] matrixStats_0.8.1     mclust_4.1            methylumi_2.6.1
> mgcv_1.7-24
> [17] minfi_1.6.0           multtest_2.16.0       nleqslv_2.0
> nlme_3.1-109
> [21] nor1mix_1.1-4         preprocessCore_1.22.0 R.methodsS3_1.4.2
> RCurl_1.95-4.1
> [25] reshape_0.8.4         siggenes_1.34.0       splines_3.0.1
> stats4_3.0.1
> [29] survival_2.37-4       tools_3.0.1           XML_3.95-0.2
>  xtable_1.7-1
> [33] zlibbioc_1.6.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>

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