[BioC] HumanRef-8_V3

[Tarca, Adi]

Yes, there are a few differences between these 2 files. There are 5
probes in the bgx version that are not in the txt version of the
HumanRef-8_V3_0_R0_11282963 manifest.

> length(intersect(fromBGX$ProbeID, fromTXT$Array_Address_Id))
[1] 24526
> setdiff(fromBGX$ProbeID, fromTXT$Array_Address_Id)
[1] 2230095  290491  450670 5360291 6250095
> setdiff(fromTXT$Array_Address_Id,fromBGX$ProbeID)
integer(0)


Adi



-----Original Message-----
From: Lynn Amon [mailto:lamon at fhcrc.org] 
Sent: Friday, May 30, 2008 2:22 PM
To: Tarca, Adi
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] HumanRef-8_V3

Hmmm... There seems to be a difference with the .bgx files and .txt 
files on the illumina.com site.  In HumanRef-8_V3_0_R0_11282963_A.txt 
there is no probe ID 6250095 but there is such a probe on 
MouseRef-8_V2_0_R0_11278551_A.txt (gene = LOC654426).  The probe ID for 
TXN in HumanRef-8_V3_0_R0_11282963_A.txt is 4290543.  I don't have 
access to a conversion tool for the bgx files.  Would anyone be willing 
to take a look at the differences between bgx and txt files? 
Lynn


Tarca, Adi wrote:
> 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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