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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

-- 
Eric Zollars MD, PhD
Fellow, Division of Rheumatology
The Johns Hopkins Hospital

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