[BioC] Fwd: Annotation discrepancy

[James W. MacDonald]

Hi Eric,

Most if not all of those probes are the oligo-dT probes that surround 
the chip (and I believe there are some in the middle as well). These 
probes are used by the scanner as 'landing lights' to allow the scanner 
to accurately align to the array prior to doing the scan.

The scanner does collect data from these probes, which ends up in the 
cel file, but they are then ignored when the array is processed further.

Best,

Jim


On 12/20/2013 1:28 PM, Eric Zollars wrote:
> All-
>
> I have been attempting to compare sequences on the HGU133 Plus 2.0 chip to
> the HT HGU 133+ PM.
> I am doing this to compare values of vectors in frma.
>
> The HT chip is a subset of HGU133 Plus 2.0 with mismatch probes removes and
> some probesets reduced in size.
>
> Looking at the probe package:
>
> hthgu133pluspmprobe$sequence: 519370
>
> However, when looking at an Affybatch object made from HT CEL files:
> Taking an Affybatch object: 'dat'
>
> Index <- pmindex(dat)
> tv = unlist(Index)
> length(tv)   #536460
>
> It appears that the Affybatch reports that there are 536460 sequences and
> the hthgu133pluspmprobe package is reporting only 519370.
>
> What is the difference?  It is possible to find the information on the
> 17090 sequences not in the hthgu133pluspmprobe package?
>
> Thanks for any information or direction.
>
> Eric Zollars
>
> Session info below: bioconductor 2.13, R 3.0.2
>
>> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: i386-w64-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] affy_1.40.0                hthgu133pluspmcdf_2.13.0
> hgu133plus2frmavecs_1.3.0
> [4] hgu133plus2probe_2.13.0    hthgu133pluspmprobe_2.13.0
> AnnotationDbi_1.24.0
> [7] Biobase_2.22.0             BiocGenerics_0.8.0
> BiocInstaller_1.12.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.30.0         DBI_0.2-7             IRanges_1.20.6
> [4] preprocessCore_1.24.0 RSQLite_0.11.4        stats4_3.0.2
> [7] tools_3.0.2           zlibbioc_1.8.0
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099