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: >>>>>>>>>>>> librarypd.hugene.2.0.st) >>>>>>>>>>>> conn<- dbpd.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() >>>>>>>>>>>> forpd.pkg.name in pd.packages) { >>>>>>>>>>>> try({ >>>>>>>>>>>> requirepd.pkg.name, character.only=TRUE) || stop("Can't >>>>>>>>>>>> load >>>>>>>>>>>> the >>>>>>>>>>>> pd.package") >>>>>>>>>>>> conn<- db(getpd.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]] >>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Bioconductor mailing list >>>>>>>>>>>> Bioconductor at r-project.org >>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>>>>> Search the archives: >>>>>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>> >>>>>>> >>>>> >>> >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor