Dear list,

I am trying to analyze Affymetrix HT HG-U133+ PM Array Plate data.  I found
some discrepancies between cdf and probe packages. In fact for some
probesets, the cdf package contains more information than the probe package.
These probesets are apparently control ones, but is it still expected? (I
did not find  any difference in HG-U133Plus2 array)

Thanks a lot for your help

Kind regards

Marianne

> sizePSinCDFnotinProbe

AFFX-NONSPECIFICGC10_AT AFFX-NONSPECIFICGC11_AT AFFX-NONSPECIFICGC12_AT

                    952                     960                     973

AFFX-NONSPECIFICGC13_AT AFFX-NONSPECIFICGC14_AT AFFX-NONSPECIFICGC15_AT

                    968                     960                     949

AFFX-NONSPECIFICGC16_AT AFFX-NONSPECIFICGC17_AT AFFX-NONSPECIFICGC18_AT

                    963                     942                     912

AFFX-NONSPECIFICGC19_AT AFFX-NONSPECIFICGC20_AT AFFX-NONSPECIFICGC21_AT

                    849                     813                     697

AFFX-NONSPECIFICGC22_AT AFFX-NONSPECIFICGC23_AT AFFX-NONSPECIFICGC24_AT

                    585                     407                     268

AFFX-NONSPECIFICGC25_AT  AFFX-NONSPECIFICGC3_AT  AFFX-NONSPECIFICGC4_AT

                      9                      25                     322

 AFFX-NONSPECIFICGC5_AT  AFFX-NONSPECIFICGC6_AT  AFFX-NONSPECIFICGC7_AT

                    703                     873                     914

 AFFX-NONSPECIFICGC8_AT  AFFX-NONSPECIFICGC9_AT         AFFX-R2-TAGA_AT

                    940                     959                      11

        AFFX-R2-TAGB_AT         AFFX-R2-TAGC_AT         AFFX-R2-TAGD_AT

                     11                      11                      11

        AFFX-R2-TAGE_AT         AFFX-R2-TAGF_AT         AFFX-R2-TAGG_AT

                     11                      11                      11

        AFFX-R2-TAGH_AT      AFFX-R2-TAGIN-3_AT      AFFX-R2-TAGIN-5_AT

                     11                      11                      11

     AFFX-R2-TAGIN-M_AT       AFFX-R2-TAGJ-3_AT       AFFX-R2-TAGJ-5_AT

                     11                      11                      11

      AFFX-R2-TAGO-3_AT       AFFX-R2-TAGO-5_AT       AFFX-R2-TAGQ-3_AT

                     11                      11                      11

      AFFX-R2-TAGQ-5_AT

                     11

> unlist(lapply(PRinfoPSinCDFnotinProbe_spl, nrow))

AFFX-NONSPECIFICGC10_AT AFFX-NONSPECIFICGC11_AT AFFX-NONSPECIFICGC12_AT

                      1                       1                       1

AFFX-NONSPECIFICGC13_AT AFFX-NONSPECIFICGC14_AT AFFX-NONSPECIFICGC15_AT

                      1                       1                       1

AFFX-NONSPECIFICGC16_AT AFFX-NONSPECIFICGC17_AT AFFX-NONSPECIFICGC18_AT

                      1                       1                       1

AFFX-NONSPECIFICGC19_AT AFFX-NONSPECIFICGC20_AT AFFX-NONSPECIFICGC21_AT

                      1                       1                       1

AFFX-NONSPECIFICGC22_AT AFFX-NONSPECIFICGC23_AT AFFX-NONSPECIFICGC24_AT

                      1                       1                       1

AFFX-NONSPECIFICGC25_AT  AFFX-NONSPECIFICGC3_AT  AFFX-NONSPECIFICGC4_AT

                      1                       1                       1

 AFFX-NONSPECIFICGC5_AT  AFFX-NONSPECIFICGC6_AT  AFFX-NONSPECIFICGC7_AT

                      1                       1                       1

 AFFX-NONSPECIFICGC8_AT  AFFX-NONSPECIFICGC9_AT         AFFX-R2-TAGA_AT

                      1                       1                       1

        AFFX-R2-TAGB_AT         AFFX-R2-TAGC_AT         AFFX-R2-TAGD_AT

                      1                       1                       1

        AFFX-R2-TAGE_AT         AFFX-R2-TAGF_AT         AFFX-R2-TAGG_AT

                      1                       1                       1

        AFFX-R2-TAGH_AT      AFFX-R2-TAGIN-3_AT      AFFX-R2-TAGIN-5_AT

                      1                       1                       1

     AFFX-R2-TAGIN-M_AT       AFFX-R2-TAGJ-3_AT       AFFX-R2-TAGJ-5_AT

                      1                       1                       1

      AFFX-R2-TAGO-3_AT       AFFX-R2-TAGO-5_AT       AFFX-R2-TAGQ-3_AT

                      1                       1                       1

      AFFX-R2-TAGQ-5_AT

                      1

The corresponding code is below:

library*(*affy*)*

library*(*hthgu133pluspmcdf*)*

library*(*hthgu133pluspmprobe*)*

PSn *<-* ls*(*hthgu133pluspmcdf*)*

PSHT *<-* mget*(*PSn, hthgu133pluspmcdf*)*

names*(*PSHT*)* *<-* toupper*(*names*(*PSHT*))*

cdfInfo *<-* unlist*(*lapply*(*PSHT, *function**(*el*){*el*[*,1*]**}))*

cdfInfo *<-* paste*(*cdfInfo, sub*(*"_AT\\w*$", "_AT", names*(*cdfInfo*))*,
sep = "."*)*

PSn *<-* toupper*(*PSn*)*

HTprobe *<-* as.data.frame*(*hthgu133pluspmprobe*)*

HTprobe*$*abs *<-* xy2indices*(*HTprobe*$*x, HTprobe*$*y, nr = 744*)*

HTprobe*$*Probe.Set.Name <http://probe.set.name/> *<-* toupper*(*HTprobe*$*
Probe.Set.Name <http://probe.set.name/>*)*

ProbeInfo *<-* paste*(*HTprobe*$*abs,
HTprobe*$*Probe.Set.Name<http://probe.set.name/>,
sep = "."*)*

length*(*unlist*(*lapply*(*PSHT, *function**(*el*){*el*[*,1*]**})))* *==*length
*(*HTprobe*$*abs*)* ## FLAG!!

length*(*intersect*(*ProbeInfo, cdfInfo*))*

length*(*setdiff*(*ProbeInfo, cdfInfo*))*

length*(*setdiff*(*cdfInfo, ProbeInfo*))*

## in common 519200 probe absolute positions

PSlocinCDFnotinProbe *<-* setdiff*(*cdfInfo, ProbeInfo*)*

PSinCDFnotinProbe *<-* unique*(*sub*(*"^.*\\.", "", PSlocinCDFnotinProbe*))*

sizePSinCDFnotinProbe *<-* listLen*(*PSHT*[*PSinCDFnotinProbe*]**)*/2

names*(*sizePSinCDFnotinProbe*)* *<-* PSinCDFnotinProbe

PRinfoPSinCDFnotinProbe *<-*
HTprobe*[*HTprobe*$*Probe.Set.Name<http://probe.set.name/>%in%
PSinCDFnotinProbe,
*]*

PRinfoPSinCDFnotinProbe_spl *<-* split*(*PRinfoPSinCDFnotinProbe,
PRinfoPSinCDFnotinProbe*$*Probe.Set.Name <http://probe.set.name/>*)*

unlist*(*lapply*(*PRinfoPSinCDFnotinProbe_spl, nrow*))*



PS: my sessionInfo is:

>sessionInfo()

R version 2.9.0 (2009-04-17)

i386-pc-mingw32

locale:

LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:

[1] hthgu133pluspmprobe_2.4.0 AnnotationDbi_1.6.1

[3] hthgu133pluspmcdf_2.4.0   affy_1.22.0

[5] Biobase_2.4.1

loaded via a namespace (and not attached):

[1] affyio_1.12.0        DBI_0.2-4            preprocessCore_1.6.0

[4] RSQLite_0.7-1        tools_2.9.0

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