Dear Gilbert,

Thanks for a prompt reply. I am extremely sorry because I forgot to remove the following line

"Apparently there are some difference between annotating with illuminaHumanv3BeadID.db and lumiHumanAll.db."

It will be great if you kindly have a look at the questions at the bottom of the mail.

This is the session details :

R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
  [1] limma_3.2.1                    illuminaHumanv3BeadID.db_1.2.0
  [3] lumiHumanAll.db_1.6.1          lumiHumanIDMapping_1.2.1
  [5] lumi_1.10.2                    RSQLite_0.7-3
  [7] DBI_0.2-4                      preprocessCore_1.6.0
  [9] mgcv_1.5-6                     affy_1.22.1
[11] annotate_1.22.0                AnnotationDbi_1.6.1
[13] Biobase_2.4.1                  session_1.0.2

loaded via a namespace (and not attached):
[1] affyio_1.12.0   grid_2.9.0      lattice_0.17-26 nlme_3.1-96
[5] xtable_1.5-5



On 12/10/2009 06:12 PM, Gilbert Feng wrote:

> Hi, Mamun
>
> Thanks for your information.
>
> probeID2nuID calls "lumiHumanIDMapping", not "lumiHumanAll.db". The latter
> one only provides the mapping between nuIDs (based on probe sequences) and
> annotations in org.Hs.eg.db  The mapping between Illumina IDs and nuIDs
> requires "lumiHumanIDMapping" package.
>
> Could you show us your sessionInfp()?
>
> Best
>
> Gilbert
>
> On 12/10/09 9:04 AM, "Md.Mamunur Rashid"<mamunur.rashid@kcl.ac.uk>  wrote:
>
>    
>> Dear List,
>>
>> I am trying to annotate some illumina microarray probes (humanHT12v3) from an
>> experiment of 96 samples.
>> Here is what I have done in brief
>>
>> 1. I have read and processed(also includes detection p.value filtering) the
>> raw data file with lumi package
>> 2. Found some differentially expressed genes using linear model
>>
>> Now in my topTable I have some thing like that
>>
>>      
>>>   top<- topTable(aneu348_fit2,coef=2,adjust="BH")
>>>   top
>>>        
>>              ID      logFC  AveExpr         t      P.Value  adj.P.Val        B
>> 19287  730612  0.1968519 6.506182  5.446788 1.729911e-06 0.03507526 4.750244
>> 19897 3520463  0.3286017 7.057259  5.390423 2.103278e-06 0.03507526 4.580566
>> 3028  2650605  0.4613558 7.115252  5.309757 2.780147e-06 0.03507526 4.338214
>> 3956  3310538  0.5527499 8.000359  5.113185 5.466881e-06 0.05172900 3.750403
>> 1626  3390605 -0.2277937 6.930935 -4.890353 1.168046e-05 0.07558592 3.089894
>> 25875 6280470  0.5706626 7.235376  4.841339 1.378711e-05 0.07558592 2.945587
>> 34978 6760546  0.3195073 7.659098  4.783197 1.677400e-05 0.07558592 2.774918
>> 32380 3940692 -0.2995773 8.258397 -4.756620 1.834288e-05 0.07558592 2.697098
>> 35264 1740020 -0.3454641 7.384281 -4.734429 1.976252e-05 0.07558592 2.632216
>> 33126 6040398  0.5112817 7.517186  4.731312 1.997039e-05 0.07558592 2.623109
>>
>>
>> Then, I try to annotate top IDs with geneName, geneSymbol , EntrezId and
>> others.
>>
>>
>> ** As you can see from the result of the topTable my probeIDs are the
>> array_Address_ID (according to manifest file buy illumina
>> HumanHT-12_v3_0_R2_11283641_A)
>>
>>
>>      
>>>    geneSymbol<- getSYMBOL(, 'illuminaHumanv3BeadID.db')
>>>    geneName<- sapply(lookUp(aneu348_probeList, 'illuminaHumanv3BeadID.db',
>>> 'GENENAME'), function(x) x[1])
>>>        
>>    gives me the correct geneName and Symbol. (according to the manifest file)
>>
>>    But when I try to convert these probeIDs using IlluminaID2nuID() or
>> probeID2nuID() method
>>    it transforms to a complete different set of geneNames and symbol.
>>
>> I then added "000" before all of my probes and passed it to IllumimnaID2nuID()
>> function
>>
>>      
>>>   top<- paste("000",top,sep="")
>>>   illu<- IlluminaID2nuID(top)
>>>        
>> Warning messages:
>> 1: In getChipInfo(IlluminaID, lib.mapping = lib.mapping, species = species,  :
>>     Some input IDs can not be matched!
>>
>> 2: In if (!is.na(chipInfo$IDType)) { :
>>     the condition has length>   1 and only the first element will be used
>>
>>
>>      
>>>   illu[1,]         # Here illu[1,] holds the mapping for "000730612"
>>>        
>> Search_Key        ILMN_Gene        Accession           Symbol
>>                 NA               NA               NA               NA
>>           Probe_Id Array_Address_Id             nuID
>>                 NA               NA               NA
>>
>> now for some reason it is always showing "NA" for few of the probes even
>> though when I passed
>> them individually to the function it returns the correct mapping
>>
>>      
>>>   IlluminaID2nuID(top[1])     # here  top[1] = "000730612"
>>>        
>>    Search_Key   ILMN_Gene Accession     Symbol  Probe_Id
>> 000730612 "ILMN_10981" "HTRA1"   "NM_002775.3" "HTRA1" "ILMN_1676563"
>>             Array_Address_Id nuID
>> 000730612 "000730612"      "ZEObIyCCVRqJSjqHrY"
>>
>> So my questions are :
>>
>> 1. Why the above functions can not find any entry for some of the  probeIDs even though
>> it's present ? (e.g. 000730612 )
>>      
>> 2. The way around I found out (adding "000" in the beginning) , is it correct
>> or there are
>>      some other better options ?
>>
>> 3. Even though it's a Human-HT12 chip , the getChipInfo() gives
>>
>>      getChipInfo(aneu348_N)
>>      $chipVersion
>>      [1] "HumanWG6_V2_11223189_B"
>>
>>
>> 4. I am trying to develop a workflow which will handle data with both type of
>> probeID
>>      pattern(ie. "ILMN_1805" or "730612"). What would be the standard path way
>> to annotate
>>      both type of data?
>>
>>
>> Please accept my apology if the mail seems long. I tried to provide as mush
>> details as I could
>>
>> thanks in advance,
>>
>> regards,
>> Mamun
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
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>>
>>      
>
> -----------------------------------------------
> Gang (Gilbert) Feng, PhD
> Biomedical Informatics Center
> Robert H. Lurie Comprehensive Cancer Center
> Northwestern University
> 750 N. Lake Shore Drive, 11th Floor(11-175e)
> Chicago, IL  60611
> Phone:312-503-2358
> Email g-feng (at) northwestern.edu
> -----------------------------------------------
>
>
>
>    


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