[BioC] HumanRef-8_V3

[Tarca, Adi]

Hi Lynn,

As I said in the first e-mail, the array is HumanRef-8_V3 array. This is
an array with 8 slots for 8 different samples.
According to the HumanRef-8_V3_0_R0_11282963_A.bgx from Illumina for
this chip, this probe has "TXN" as gene symbol and is called Thioredoxin
mRNA. The accession is NM_003329.1
It is true though that it has a missing Entrez ID. I will send you an
array so you can look at it.


Regards,
Adi




-----Original Message-----
From: Lynn Amon [mailto:lamon at fhcrc.org] 
Sent: Friday, May 30, 2008 1:44 PM
To: Tarca, Adi
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] HumanRef-8_V3

Hi Adi,
That issue wasn't clear from your first email.  If probe IDs are 
missing, that is a bug.  I don't see ProbeID = 6250095 anywhere in the 
illumina annotation package for Human v3.  I do find it in the Mouse v2 
array though.  What accession id did you find for it?  Can you send me a

list of probe IDs that are missing.  I don't have any V3 arrays to test.
Thanks,
Lynn


Tarca, Adi wrote:
> Hi Lynn,
> I am aware that these packges work with probe IDs and not with target
> IDs. However there are probe IDs on the HumanRef-8_V3 that could not
be
> found in  either two packages lumiHumanAll.db and
> illuminaHumanv3ProbeID.db.
>
> e.g:
>   
>> x<-illuminaHumanv3ProbeIDSYMBOL
>> aT1$Symbol<-as.vector(unlist( as.list(x[aT1$ID]) ))
>>     
> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : 
>   value for "6250095" not found
>
> However I was able to build my own annotation package using
> makeHUMANCHIP_DB function.
>
> Thanks,
> Adi
>
>
> -----Original Message-----
> From: Lynn Amon [mailto:lamon at fhcrc.org] 
> Sent: Friday, May 30, 2008 12:55 PM
> To: Tarca, Adi
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] HumanRef-8_V3
>
> The illumina annotation packages use the probe ID rather than the
target
>
> id output by illumina's analysis software.  If you use the .txt or
.csv 
> files output by the scanner, you will have probe IDs that match the 
> existing annotation packages.
> Lynn Amon
>
>
> Tarca, Adi wrote:
>   
>> Hi all,
>>
>> Did anyone make a package for the Illumina HumanRef-8_V3 array?
>> I have tried both lumiHumanAll.db and illuminaHumanv3ProbeID.db but
>>     
> they
>   
>> no not recognize the IDs on this array.
>>
>> Thanks,
>>
>> Adi Tarca
>>
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