atarca at med.wayne.edu
Fri May 30 19:56:42 CEST 2008
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.
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
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.
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
> found in either two packages lumiHumanAll.db and
>> 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.
> -----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
> id output by illumina's analysis software. If you use the .txt or
> 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
>> no not recognize the IDs on this array.
>> Adi Tarca
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> Search the archives:
More information about the Bioconductor