[BioC] question regarding lumiHumanV1SUMFUNC and lumiRatV1SUMFUNC in lumiHumanV1 and lumiRatV1, respectively

[James W. MacDonald]

Hi Chao-Jen,

chaochao wong wrote:
> I installed the Illumina Sentrix RatRef-12 v1 Expression Beadchip annotation
> data and sentrix Human Ref-8 v1. I was trying to get the mapping between the
> nuID (manufacturer identifiers?) and Gene Function summaries. But I did not
> valid mapping. Did I do anything wrong?  The following are the examples that
> I did earlier in which I did not get the mapping.

You didn't do anything wrong (unless you count not checking to see if 
there are any mappings in the first place).

 > lumiHumanV1()


Quality control information for  lumiHumanV1
Date built: Created: Wed Mar 28 22:41:10 2007

Number of probes: 37715
Probe number missmatch: None
Probe missmatch: None
Mappings found for probe based rda files:
	 lumiHumanV1ACCNUM found 26093 of 37715
	 lumiHumanV1CHRLOC found 18654 of 37715
	 lumiHumanV1CHR found 19261 of 37715
	 lumiHumanV1ENTREZID found 19264 of 37715
	 lumiHumanV1ENZYME found 2148 of 37715
	 lumiHumanV1GENENAME found 18188 of 37715
	 lumiHumanV1GO found 16778 of 37715
	 lumiHumanV1MAP found 19166 of 37715
	 lumiHumanV1OMIM found 12698 of 37715
	 lumiHumanV1PATH found 4635 of 37715
	 lumiHumanV1PMID found 19007 of 37715
	 lumiHumanV1REFSEQ found 19264 of 37715
	 lumiHumanV1SUMFUNC found 0 of 37715
	 lumiHumanV1SYMBOL found 19264 of 37715
	 lumiHumanV1UNIGENE found 19029 of 37715
Mappings found for non-probe based rda files:
  	 lumiHumanV1CHRLENGTHS found 25
	 lumiHumanV1ENZYME2PROBE found 785
	 lumiHumanV1GO2ALLPROBES found 8265
	 lumiHumanV1GO2PROBE found 6093
	 lumiHumanV1ORGANISM found 1
	 lumiHumanV1PATH2PROBE found 192
	 lumiHumanV1PFAM found 15284
	 lumiHumanV1PMID2PROBE found 139947
	 lumiHumanV1PROSITE found 10797
Mappings from Illumina Identifiers to nuIDs:
	lumiHumanV1PROBEID2NUID: from Illumina Probe Id to nuID
	lumiHumanV1TARGETID2NUID: from Illumina Target Id to nuID


The relevant line being this one:

	 lumiHumanV1SUMFUNC found 0 of 37715

Which indicates that there are no mappings from nuID to function, hence 
all are NA.

Best,

Jim



> 
>> yy<-as.list(lumiHumanV1SUMFUNC);
> 
>> yy[300]
> $QUTclLhfjS9RJSk8KY
> [1] NA
> 
>> yy[1:3]
> $x00WAIBIVaMvS3EVQ0
> [1] NA
> 
> $`9iFKOnl5SKK4SnkAS8`
> [1] NA
> 
> $Ke_INOf6KSdNz6Qeek
> [1] NA
> 
>> yy[3000]
> $EToSUJUoCKV4UBcUcw
> [1] NA
> 
>>  yy<-as.list(lumiRatV1SUMFUNC);
>> yy[400:405]
> $ZKh4qJeJqX78SffVx0
> [1] NA
> 
> $fZ4ITQkgUr9REl7VUo
> [1] NA
> 
> $TnuS_X97qhDNNBR9F4
> [1] NA
> 
> $BjKLnfM6.o7jlXyK3U
> [1] NA
> 
> $`9R3oyEUo0eyUTlV9eU`
> [1] NA
> 
> $EFSKRSiL6IITfqUik0
> [1] NA
> 
> Thanks a lot for the help.
> 
> 
> Cheers,
> ---
> Chao-Jen Wong
> Postdoctoral Researcher
> Computational Science Research Center
> San Diego State University
> http://www.csrc.sdsu.edu
> Office Tel: 691.594.2258
> 
> 	[[alternative HTML version deleted]]
> 
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