Dear All,

I am using the Illumina Spike-in beadarrays data set, and
I have read the re-annotation for non-spikes and non controls from here: http://compbio.sysbiol.cam.ac.uk/Resources/spike/data/NewAnnotationM1.txt
and there are 46005 probes.


On the other hand, from the bead studio output (from the website above), in SampleProbeProfile.txt file, there are 47456 probes.


Currently, I use the SampleProbeProfile.txt file and it gives me a problem when I want to use the probe sequences on the data set.
There are some probes which I don't know how to get to know about their sequences. 
(To get the probe sequences, I mapped the probeID to its nuID and from the nuID thenI retrieved the probe sequences. If this is not the right thing to do, please let me know. ).
My questions:
a. what should I do to know about some probes sequence of the Illumina Spike-in data set, please?
    May be there is another source than the link above that I could visit. 
b. if there is no way to know about their probe sequences, is it permissible to delete those probes from further analysis, please? Or ... should I use the new annotation only.
c. the spike in experiment of the Affymetrix is available at SpikeIn package. Is there a similar package for the Illumina Spike in, please? (I did not check it yet)

Below, I explain what I have done. It's quite long, apologise for that.
Please let me know if I have made the mistake(s) or there are things that I missed on the steps.

For any help, thank you very much in advance.

With kind regards,
R Fajriyah

=====================================================================================================================


library(lumi)
library(lumiMouseIDMapping)
library(lumiMouseAll.db)

rbs<-read.table("~/.../spike_beadstudio_output/SampleProbeProfile.txt",header=T,sep="\t") #### regular probes from the website above
cns<-read.table("~/.../spike_beadstudio_output/ControlProbeProfile.txt",header=T,sep="\t") #### control probes
narbs<-read.table("~/.../NewAnnotationM1.txt",header=T,sep="\t") #### new annotation of the regular probes
> c(dim(rbs),dim(cns),dim(narbs)) #### dim of regular and control probes
[1] 47456  194  1721  19446005    21
> csp<-cns[17:49,1:3] #### retrieve the spike-in probes only
> rbs1<-rbs[, 1:3] #### regular probes (non-spikes and non controls) only
> rbss<-rbind(rbs1,csp)
> pidr<-rbss[,2] #### retrieve the probeID
> nuidr<-probeID2nuID(pidr, lib='lumiMouseIDMapping') #### I realized that I could not find the nuID for some of the ProbesID
Warningmessage:
IngetChipInfo(IlluminaID, lib.mapping= lib.mapping, species= species,  :
  SomeinputIDscannotbematched!

> nuidr1h<-probeID2nuID(pidr[1:100], lib='lumiMouseIDMapping') #### I already checked that the first 100 probes, are okay
> nuidr1h15<-probeID2nuID(pidr[101:115], lib='lumiMouseIDMapping') #### some probes after 100th don't have nuID
Warningmessage:
IngetChipInfo(IlluminaID, lib.mapping= lib.mapping, species= species,  :
  SomeinputIDscannotbematched!

> nuidr1h15#### I checked which one ...
          Search_key       Target             ProbeId     Accession Symbol nuID                
2470008   NA               NA                 NA          NA        NA     NA                  
107000471"9626096_327_rc""9626096_327_rc-S""107000471"""        ""    "NqCSCZmBIJiCSnj68M"
104120113"9626096_327"    "9626096_327-S"    "104120113"""        ""    "64PBQ0l592fe9mZ958"
101850133"9626096_331_rc""9626096_331_rc-S""101850133"""        ""    "E8_jEasVqYdLc2ih6Y"
5690687   NA               NA                 NA          NA        NA     NA                  
106450575"9626096_5_rc"  "9626096_5_rc-S"  "106450575"""        ""    "BI1aGJVQOAhVYhqy0M"
104280750"9626096_5"      "9626096_5-S"      "104280750"""        ""    "9j4cVt2qt.T_qnbWo0"
101240091"9626096_7"      "9626096_7-S"      "101240091"""        ""    "xjeiFXlSoUWFRRaisI"
100840706"9626100_15"    "9626100_15-S"    "100840706"""        ""    "oUNL2fdn3vZmfWd1ic"
101170112"9626100_20_rc"  "9626100_20_rc-S"  "101170112"""        ""    "uoEmIUY9o5ASQin8_o"
770541    NA               NA                 NA          NA        NA     NA                  
103710377"9626100_224_rc""9626100_224_rc-S""103710377"""        ""    "NmZgSCYgmB4_vL0DCs"
103870242"9626100_224"    "9626100_224-S"    "103870242"""        ""    "ZXz_BwUNL2fdn3vZmc"
104540048"9626100_230_rc""9626100_230_rc-S""104540048"""        ""    "6dUKBJiFGPaOQEkIp8"
2190154   NA               NA                 NA          NA        NA     NA                  
> nuidr101<-probeID2nuID(pidr[101], lib='lumiMouseIDMapping') #### I tried a single mapping and it worked
> nuidr101
     Search_Key   ILMN_Gene Accession    Symbol  Probe_Id     Array_Address_Id nuID         
2470008 "ILMN_194227" "BMP8B"   "NM_007559.4" "Bmp8b" "ILMN_1229350" "002470008"    "cXghVQQPiHAVLKfdqE"

> nuidr105<-probeID2nuID(pidr[105], lib='lumiMouseIDMapping') #### it worked too for this probeID
> nuidr105
     Search_Key   ILMN_Gene Accession    Symbol   Probe_Id     Array_Address_Id nuID         
5690687 "ILMN_220120" "INPP5A"  "NM_183144.1" "Inpp5a" "ILMN_2717861" "005690687"    "icS9ejqmimYvDtr9XI"

> nuidr1011<-probeID2nuID(pidr[111], lib='lumiMouseIDMapping') #### it did not work for this probeID
Warningmessage:
IngetChipInfo(IlluminaID, lib.mapping= lib.mapping, species= species,  :
  Nomatcheswerefound!

> nuidr1011
770541 
    NA 
> nuidr1015<-probeID2nuID(pidr[115], lib='lumiMouseIDMapping') #### it worked too for this probeID
> nuidr1015
     Search_Key   ILMN_Gene Accession    Symbol   Probe_Id     Array_Address_Id nuID         
2190154 "ILMN_217818" "DNAJA2"  "NM_019794.1" "Dnaja2" "ILMN_3003324" "002190154"    "x7NMU3eJcMkcixP3Ik"

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attachedbasepackages:
[1] parallel  stats    graphics  grDevicesutils    datasets  methods  base     

otherattachedpackages:
[1] lumiMouseAll.db_1.22.0    org.Mm.eg.db_2.10.1      lumiMouseIDMapping_1.10.0
[4] RSQLite_0.11.4            DBI_0.2-7                AnnotationDbi_1.24.0     
[7] lumi_2.14.0              Biobase_2.22.0            BiocGenerics_0.8.0       

loadedviaanamespace (andnotattached):
 [1] affy_1.40.0            affyio_1.30.0          annotate_1.40.0        base64_1.1           
 [5] beanplot_1.1          BiocInstaller_1.12.0  biomaRt_2.18.0        Biostrings_2.30.0     
 [9] bitops_1.0-6          BSgenome_1.30.0        bumphunter_1.2.0      codetools_0.2-8       
[13] colorspace_1.2-4      digest_0.6.3          doRNG_1.5.5            foreach_1.4.1         
[17] genefilter_1.44.0      GenomicFeatures_1.14.0GenomicRanges_1.14.1  grid_3.0.2           
[21] illuminaio_0.4.0      IRanges_1.20.0        iterators_1.0.6        itertools_0.1-1       
[25] KernSmooth_2.23-10    lattice_0.20-24        limma_3.18.0          locfit_1.5-9.1       
[29] MASS_7.3-29            Matrix_1.0-14          matrixStats_0.8.12    mclust_4.2           
[33] methylumi_2.8.0        mgcv_1.7-27            minfi_1.8.0            multtest_2.18.0       
[37] nleqslv_2.0            nlme_3.1-111           nor1mix_1.1-4          pkgmaker_0.17.4       
[41] preprocessCore_1.24.0  R.methodsS3_1.5.2      RColorBrewer_1.0-5    RCurl_1.95-4.1       
[45] registry_0.2          reshape_0.8.4          rngtools_1.2.3        Rsamtools_1.14.1     
[49] rtracklayer_1.22.0    siggenes_1.36.0        splines_3.0.2          stats4_3.0.2         
[53] stringr_0.6.2          survival_2.37-4        tools_3.0.2            XML_3.95-0.2          
[57] xtable_1.7-1          XVector_0.2.0          zlibbioc_1.8.0       
> 
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