[BioC] pd.hugene.2.0.st missing normgene->exon mappings
James W. MacDonald
jmacdon at uw.edu
Tue Jul 9 19:13:58 CEST 2013
Hi Mark,
Thanks for the heads-up. We already knew that Affy messed up the
transcript and probeset annotation files (and had them fixed), but
didn't think I needed to check the others. Famous last words, no?
> x <- readPgf("HuGene-2_0-st.pgf")
> table(x$probesetType)
control->affx control->affx->bac_spike
18 18
control->affx->ercc_spike control->affx->polya_spike
92 39
control->bgp->antigenomic main
23 349012
normgene->intron reporter
3575 82
> y <- read.csv("HuGene-2_0-st-v1.na33.2.hg19.transcript.csv",
comment.char = "#", stringsAsFactors=FALSE, header = TRUE)
> table(y$category)
control->affx control->affx->bac_spike
18 18
control->affx->ercc-spike control->affx->polya_spike
92 39
control->bgp->antigenomic main
23 44629
normgene->exon normgene->intron
1626 3575
reporter rescue
82 3515
I'll ping Affymetrix and see what they have to say.
Best,
Jim
On 7/9/2013 3:29 AM, Mark Cowley wrote:
> 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
>
>
>
>
>
> [[alternative HTML version deleted]]
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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