Dear Benilton, James & Bioconductors,
Thanks for providing the platform design packages for hugene/mogene/ragene 1.0/1.1/2.0/2.1 arrays.

I use SQL to query these packages & ultimately retain only 'main' probes in my analysis. This works well for 1.0 and 1.1 packages, but nor for 2.0 and 2.1 ST arrays. For 2.0 and 2.1 arrays, the normgene->exon control probes are misclassified as 'main' probes.

evidence: the HuGene-2_0-st-v1.na33.2.hg19.transcript.csvNetAffx csv files lists 1626 normgene->exon probes, however the pg.hugene.2.0.st package lists 0, and assigns these 1626 probes to the 'main' category:

# probe types:
library(pd.hugene.2.0.st)
conn <- db(pd.hugene.2.0.st)
dbGetQuery(conn,"SELECT * from type_dict")
   type                   type_id
1     1                      main
2     2             control->affx
3     3             control->chip
4     4 control->bgp->antigenomic
5     5     control->bgp->genomic
6     6            normgene->exon
7     7          normgene->intron
8     8  rescue->FLmRNA->unmapped
9     9  control->affx->bac_spike
10   10            oligo_spike_in
11   11           r1_bac_spike_at

# probe counts for each of the probe categories:
dbGetQuery(conn,"SELECT type, count(*) from featureSet GROUP BY type")
  type count(*)
1   NA     3728
2    1   345497
3    2       18
4    4       23
5    7     3575
6    9       18

NB: no type 6 probes.
I've tested all 12 ho/mo/ra gene 1.0,1.1,2.0,2.1 ST packages, and see this issue for all 2.0 and 2.1 arrays (see below)

Can these mappings please be updated?

PS, there's a bunch of probes with type = NA in the database. I haven't investigated these in any detail.

cheers,
Mark
-----------------------------------------------------
Mark Cowley, PhD

Genome Informatics Division & the Centre for Clinical Genomics
The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia
-----------------------------------------------------

All 12 packages below:
pd.packages <- c(
  "pd.hugene.1.0.st.v1", "pd.hugene.1.1.st.v1", "pd.hugene.2.0.st", "pd.hugene.2.1.st",
  "pd.mogene.1.0.st.v1", "pd.mogene.1.1.st.v1", "pd.mogene.2.0.st", "pd.mogene.2.1.st",
  "pd.ragene.1.0.st.v1", "pd.ragene.1.1.st.v1", "pd.ragene.2.0.st", "pd.ragene.2.1.st"
)

a <- b <- list()
for(pd.pkg.name in pd.packages) {
  try({
    require(pd.pkg.name, character.only=TRUE) || stop("Can't load the pd.package")
    conn <- db(get(pd.pkg.name))
    a[[pd.pkg.name]] <- dbGetQuery(conn,"SELECT type, count(*) from featureSet GROUP BY type")
    b[[pd.pkg.name]] <- dbGetQuery(conn,"SELECT fsetid from featureSet WHERE type = 6")[,1]
  })
}
dbGetQuery(conn,"SELECT * from type_dict")

> a
$pd.hugene.1.0.st.v1
  type count(*)
1   NA      227
2    1   253002
3    2       57
4    4       45
5    6     1195
6    7     2904

$pd.hugene.1.1.st.v1
  type count(*)
1   NA      227
2    1   253002
3    2       57
4    4       45
5    6     1195
6    7     2904

$pd.hugene.2.0.st
  type count(*)
1   NA     3728
2    1   345497
3    2       18
4    4       23
5    7     3575
6    9       18

$pd.hugene.2.1.st
  type count(*)
1   NA     3728
2    1   345497
3    2       18
4    4       23
5    7     3575
6    9       18

$pd.mogene.1.0.st.v1
  type count(*)
1   NA       86
2    1   234878
3    2       21
4    4       45
5    6     1324
6    7     5222

$pd.mogene.1.1.st.v1
  type count(*)
1   NA       86
2    1   234878
3    2       21
4    4       45
5    6     1324
6    7     5222

$pd.mogene.2.0.st
  type count(*)
1   NA      810
2    1   263551
3    2       18
4    4       23
5    7     5331
6    9       18

$pd.mogene.2.1.st
  type count(*)
1   NA      810
2    1   263551
3    2       18
4    4       23
5    7     5331
6    9       18

$pd.ragene.1.0.st.v1
  type count(*)
1   NA      254
2    1   211195
3    2       21
4    4       45
5    6      399
6    7     1153

$pd.ragene.1.1.st.v1
  type count(*)
1   NA      254
2    1   211195
3    2       21
4    4       45
5    6      399
6    7     1153

$pd.ragene.2.0.st
  type count(*)
1   NA     1071
2    1   214018
3    2       18
4    4       23
5    7     5083
6    9       18

$pd.ragene.2.1.st
  type count(*)
1   NA     1071
2    1   214018
3    2       18
4    4       23
5    7     5083
6    9       18

> sapply(b,length)
pd.hugene.1.0.st.v1 pd.hugene.1.1.st.v1    pd.hugene.2.0.st    pd.hugene.2.1.st
               1195                1195                   0                   0
pd.mogene.1.0.st.v1 pd.mogene.1.1.st.v1    pd.mogene.2.0.st    pd.mogene.2.1.st
               1324                1324                   0                   0
pd.ragene.1.0.st.v1 pd.ragene.1.1.st.v1    pd.ragene.2.0.st    pd.ragene.2.1.st
                399                 399                   0                   0

> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] pd.ragene.2.1.st_2.12.1   pd.ragene.2.0.st_2.12.0
 [3] pd.ragene.1.1.st.v1_3.8.0 pd.ragene.1.0.st.v1_3.8.0
 [5] pd.mogene.2.1.st_2.12.1   pd.mogene.2.0.st_2.12.0
 [7] pd.mogene.1.1.st.v1_3.8.0 pd.mogene.1.0.st.v1_3.8.0
 [9] pd.hugene.2.1.st_3.8.0    pd.hugene.1.1.st.v1_3.8.0
[11] pd.hugene.1.0.st.v1_3.8.0 pd.hugene.2.0.st_3.8.0
[13] oligo_1.24.0              Biobase_2.20.0
[15] oligoClasses_1.22.0       BiocGenerics_0.6.0
[17] RSQLite_0.11.4            DBI_0.2-7
[19] BiocInstaller_1.10.2

loaded via a namespace (and not attached):
 [1] affxparser_1.32.1     affyio_1.28.0         Biostrings_2.28.0
 [4] bit_1.1-10            codetools_0.2-8       ff_2.2-11
 [7] foreach_1.4.1         GenomicRanges_1.12.3  IRanges_1.18.1
[10] iterators_1.0.6       preprocessCore_1.22.0 splines_3.0.0
[13] stats4_3.0.0          tools_3.0.0           zlibbioc_1.6.0





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