[BioC] pd.hugene.2.0.st missing normgene->exon mappings
Mark Cowley
m.cowley at garvan.org.au
Mon Jul 22 02:59:53 CEST 2013
Hi Benilton,
That sounds like a great solution. I hope it's not too much work!
Mark
Sent from my iPhone
On 20/07/2013, at 9:25 AM, "Benilton Carvalho" <beniltoncarvalho at gmail.com> wrote:
> Hi Mark et. al.,
>
> On the initial example given by Mark, the PGF lists (a selection of)
> probes as "main", while the transcript annotation file lists them as
> "normgene->exon".
>
> I understand that Affymetrix uses probes that map to "actual stuff"
> (lack of better word, sorry) as positive controls... In this case, we
> have probes that are both "main" and "normgene->exon".
>
> On the newest designs, we are missing the annotation described in the
> transcript annotation file for the probes that belong to multiple
> classes.
>
> If I'm not missing any information, Mark's suggestion (add 'type' to
> the *_mps tables) seems appropriate. But that requires redesigning the
> db... Will investigate the best approach for this and come back with
> more on the topic soon.
>
> b
>
> On 11 July 2013 14:53, cstrato <cstrato at aon.at> wrote:
>> Dear Mark,
>>
>> This needs probably to be answered by Jim, since for me everything is ok as
>> is.
>>
>> Best regards,
>> Christian
>>
>>
>>
>> On 7/11/13 1:55 AM, Mark Cowley wrote:
>>>
>>> Hi,
>>> is it feasible to add a 'type' column to the core_mps table, using info
>>> from the transcript csv file? since 'core' implies transcript-level
>>> analysis.
>>>
>>> cheers,
>>> Mark
>>>
>>> On 11/07/2013, at 4:29 AM, cstrato <cstrato at aon.at>
>>> wrote:
>>>
>>>> Dear Mark,
>>>>
>>>> Yes, EIF3D and pos_controls mentioned have different transcript cluster
>>>> id's. However, imho this means only that they have received these additional
>>>> transcript cluster id's to be able to define them as normgene->exon.
>>>> Furthermore, in the transcript annotation file the transcript_cluster_id is
>>>> identical to the probeset_id. Thus e.g. 16934607 is used as probeset_id in
>>>> the probeset annotation file.
>>>>
>>>> I have tested a couple of normgene->exon controls and it seems that all
>>>> of them belong to real genes in the probeset csv file with the type 'main'.
>>>> Mostly, these come in groups belonging to the same exon_id, e.g. the
>>>> mentioned controls 16934607 - 16934610 all belong to exon_id 5192052 of the
>>>> EIF3D gene.
>>>>
>>>> I suppose that you use exons as normgene->exon controls which e.g. in the
>>>> case of alternative splicing are always expressed.
>>>>
>>>> Best regards,
>>>> Christian
>>>>
>>>>
>>>> On 7/10/13 12:31 PM, Mark Cowley wrote:
>>>>>
>>>>> Hi,
>>>>> I see the point you're making Christian.
>>>>> I'm offline now, so cant check this, but i assume that EIF3D and the
>>>>> pos_control meta-probeset in question have different transcript cluster
>>>>> id's. it doesn't make sense for the pos_control transcript cluster Id to be
>>>>> tagged as 'main'. My grep -f was still running when i left work to confirm
>>>>> whether all normgene->exon probesets are all deployed within different real
>>>>> genes in the probeset csv file.
>>>>>
>>>>> Cheers and thanks for looking into this
>>>>>
>>>>> Mark
>>>>>
>>>>> Sent from my iPhone
>>>>>
>>>>> On 10/07/2013, at 7:53 AM, "cstrato" <cstrato at aon.at> wrote:
>>>>>
>>>>>> Dear Jim,
>>>>>>
>>>>>> As far as I understand it, at the transcript level 16934607 is on one
>>>>>> hand part of the EIF3D transcript and on the other hand does serve as a
>>>>>> positive control. To me this seems to be no contradiction, but probably only
>>>>>> DevNet can explain.
>>>>>>
>>>>>> Best regards,
>>>>>> Christian
>>>>>>
>>>>>>
>>>>>> On 7/9/13 11:46 PM, James W. MacDonald wrote:
>>>>>>>
>>>>>>> Hi Christian,
>>>>>>>
>>>>>>> Thanks for pointing that out. There is still a bit of an inconsistency
>>>>>>> with the pd packages that should probably be corrected, as at the
>>>>>>> probeset level e.g., 16934607 is intended to measure an exon of EIF3D,
>>>>>>> whereas at the transcript level, this same probeset is intended to be
>>>>>>> a
>>>>>>> positive control (and as you note below, these probes are incorporated
>>>>>>> into a larger probeset intended to measure the EIF3D transcript).
>>>>>>>
>>>>>>> It would be nice to be able to filter out the controls like Mark
>>>>>>> attempted (and I do regularly as well).
>>>>>>>
>>>>>>> Mark - I talked with Benilton Carvalho about this, and he will take a
>>>>>>> look next week.
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Jim
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 7/9/2013 3:38 PM, cstrato wrote:
>>>>>>>>
>>>>>>>> Dear Jim,
>>>>>>>>
>>>>>>>> In xps I use as basic file for exon arrays the probeset annotation
>>>>>>>> file and then compare the data to the data from the pgf-file. Any
>>>>>>>> differences will be reported.
>>>>>>>>
>>>>>>>> I have just checked the different files for HuGene-2_0-st. If you
>>>>>>>> check as an example the following probeset_ids:
>>>>>>>> 16934607
>>>>>>>> 16934608
>>>>>>>> 16934609
>>>>>>>> 16934610
>>>>>>>>
>>>>>>>> Then you will see that the transcript annotation file lists these ids
>>>>>>>> as 'normgene->exon' and 'pos_control'. However, the probeset
>>>>>>>> annotation file lists these ids as 'main' belonging to gene EIF3D
>>>>>>>> with
>>>>>>>> transcript_cluster_id 16934583. Looking for this id in the transcript
>>>>>>>> annotation file reveals that the number of 'total_probes' is 24.
>>>>>>>> Indeed, the probeset annotation file lists 24 probesets including the
>>>>>>>> four above mentioned probeset_ids.
>>>>>>>>
>>>>>>>> This means that although these four probesets are listed in the
>>>>>>>> transcript annotation file as 'normgene->exon' the label 'main' in
>>>>>>>> the
>>>>>>>> pgf-file is correct since these probesets are part of the gene EIF3D.
>>>>>>>>
>>>>>>>> Interestingly, the pgf-file for HuGene-1_0-st has extra probesets
>>>>>>>> listed as 'normgene->exon'. However, in this case these probesets are
>>>>>>>> also listed as 'normgene->exon' in the probeset annotation file, i.e.
>>>>>>>> these probesets do not belong to any transcript listed in the
>>>>>>>> probeset
>>>>>>>> annotation file.
>>>>>>>>
>>>>>>>> Best regards,
>>>>>>>> Christian
>>>>>>>>
>>>>>>>>
>>>>>>>> On 7/9/13 8:46 PM, James W. MacDonald wrote:
>>>>>>>>>
>>>>>>>>> Hi Christian,
>>>>>>>>>
>>>>>>>>> That's not the issue. Instead, the issue is that the pgf file lists
>>>>>>>>> the
>>>>>>>>> normgene->exon probeset IDs as being 'main'. I have received a
>>>>>>>>> response
>>>>>>>>> from Affy stating that the qcc file lists the normgene->exon
>>>>>>>>> probesets
>>>>>>>>> as pos_control, but that seems orthogonal to the issue at hand.
>>>>>>>>>
>>>>>>>>>> qcc <- read.table("HuGene-2_0-st.qcc", comment.char="#",
>>>>>>>>>
>>>>>>>>> stringsAsFactors=F, header=T)
>>>>>>>>>>
>>>>>>>>>> pgf <- readPgf("HuGene-2_0-st.pgf")
>>>>>>>>>> head(qcc)
>>>>>>>>>
>>>>>>>>> probeset_id group_name probeset_name quantification_in_header
>>>>>>>>> 1 16650001 neg_control 16650001 0
>>>>>>>>> 2 16650003 neg_control 16650003 0
>>>>>>>>>
>>>>>>>>> ## get the positive controls (normgene->exon probesets) from the qcc
>>>>>>>>> file
>>>>>>>>>>
>>>>>>>>>> pos_cont <- qcc[qcc[,2] == "pos_control",1]
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ## compare to pgf file
>>>>>>>>>>
>>>>>>>>>> x <- pgf$probesetType[pgf$probesetId %in% pos_cont]
>>>>>>>>>> table(x)
>>>>>>>>>
>>>>>>>>> x
>>>>>>>>> main
>>>>>>>>> 1626
>>>>>>>>>
>>>>>>>>> So in the pgf file, these probesets are being called 'main' instead
>>>>>>>>> of
>>>>>>>>> some sort of control. How do you handle this in xps? Do you use the
>>>>>>>>> pgf
>>>>>>>>> file?
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>>
>>>>>>>>> Jim
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 7/9/2013 2:06 PM, cstrato wrote:
>>>>>>>>>>
>>>>>>>>>> Dear Jim,
>>>>>>>>>>
>>>>>>>>>> I did not really follow the discussion so I may be wrong, but if
>>>>>>>>>> you
>>>>>>>>>> mean that there is a difference between the number of 'main' types,
>>>>>>>>>> please note that number of 'main' for pgf, i.e 349012, corresponds
>>>>>>>>>> to
>>>>>>>>>> the number of 'main' in the probeset annotation file and not in the
>>>>>>>>>> transcript annotation file.
>>>>>>>>>>
>>>>>>>>>> But as I said, I may have misunderstood the problem.
>>>>>>>>>>
>>>>>>>>>> I am mainly replying because at the beginning of this year I had
>>>>>>>>>> long
>>>>>>>>>> discussions with DevNet to make sure that the annotation files for
>>>>>>>>>> the
>>>>>>>>>> 2.X arrays are correct, and in version na33.2 DevNet did correct
>>>>>>>>>> everything what I have found.
>>>>>>>>>>
>>>>>>>>>> Best regards,
>>>>>>>>>> Christian
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 7/9/13 7:13 PM, James W. MacDonald wrote:
>>>>>>>>>>>
>>>>>>>>>>> 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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>>>>>>>>>>>> Bioconductor at r-project.org
>>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>>>>>>> Search the archives:
>>>>>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>>
>>>>>>>
>>>>>
>>>
>>>
>>
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