Question: Agi4x44PreProcess: filtration of probes using filter.probes() returns an empty RGList (re-posted, due to earlier post failure)
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gravatar for Massimo Pinto
10.5 years ago by
Massimo Pinto390
Massimo Pinto390 wrote:
I am reposting this only because, from the web archive of this list, it appears that An embedded and charset-unspecified text was scrubbed... Name: not available So perhaps my message was never seen on the list, but for those who opt to receive individual message. Thank you. Massimo ---------- Forwarded message ---------- From: Massimo Pinto <pintarello@gmail.com> Date: Fri, Apr 24, 2009 at 6:02 PM Subject: Agi4x44PreProcess: filtration of probes using filter.probes() returns an empty RGList. To: bioconductor@stat.math.ethz.ch Greetings, on a BioC2.4 installation using with the Agi4x44PreProcess library, I am trying to invoke the filter.probes() filtration function to remove those not-so-good probes. Keeping in mind that my object looks like this: > dim(ddNORM) [1] 45015 4 > class(ddNORM) [1] "RGList" attr(,"package") [1] "limma" when I apply the filtration function at the R prompt, using a syntax that I am copying from the Agi4x44PreProcess manual: >ddFILT = filter.probes(ddNORM, control = TRUE, wellaboveBG = TRUE, isfound = TRUE, wellaboveNEG = TRUE, sat = TRUE, PopnOL = TRUE, NonUnifOL = T, nas = TRUE, limWellAbove = 75, limISF = 75, limNEG = 75, limSAT = 75, limPopnOL = 75, limNonUnifOL = 75, limNAS = 100, makePLOT = TRUE, annotation.package = "hgug4112a.db", flag.counts = T, targets) I am getting an empty RGList as output: FILTERING BY ControlType FLAG ------------------------------------------------------ PROBES BEFORE FILTERING: 45015 PROBES AFTER ControlType FILTERING: 43376 RAW DATA WITHOUT CONTROLS OUT : 43376 ------------------------------------------------------ FILTERING BY IsWellAboveBG filterFLAG FLAG FILTERING OPTIONS - FLAG OK = 1 - limWellAbove: 75 % PROBES BEFORE FILTERING: 43376 PROBES AFTER QC FILTERING: 0 IsNOTWellAboveBG OUT : 0 ------------------------------------------------------ [...] so it looks to me like filtration by ControlType flag works ok, but filtration via filter flag IsWellAboveBG returns an empty RGlist, which remains empty from there onwards, as it seems: > dim(ddFILT) [1] 0 4 However, looking into the variable IsWellAboveBG somewhere in my RGList ddNORM returns > ddNORM$other$gIsWellAboveBG[8165:8178,] 41745_1_3_21 41844_1_2_22 41744_1_2_23 41743_1_3_24 [1,] 1 1 1 1 [2,] 1 1 1 1 [3,] 0 0 0 0 [4,] 0 0 0 0 [5,] 1 1 1 1 [6,] 0 0 0 0 [7,] 1 1 1 1 [8,] 1 1 1 1 [9,] 1 1 1 1 [10,] 0 0 0 0 [11,] 0 0 0 0 [12,] 1 1 1 1 [13,] 1 1 1 1 [14,] 1 1 1 1 suggesting that, in ddNORM, does have some entries have value 1 for flag IsWellAboveBG. So why is filter.probes() throwing out all of my data from ddNORM, assuming none is above background? I have also tried to suppress filtation by IsWellAboveBG, but the outcome is the same upon the next filtration invoked by filter.probes(), i.e. an empty RGList. Thank you very much indeed for any clues you may have. Clearly I cannot see clearly in the use of this function. Yours Massimo Massimo Pinto Post Doctoral Research Fellow Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome http://claimid.com/massimopinto [[alternative HTML version deleted]]
agi4x44preprocess • 611 views
ADD COMMENTlink modified 10.5 years ago by Pedro Lopez-Romero120 • written 10.5 years ago by Massimo Pinto390
Answer: Agi4x44PreProcess: filtration of probes using filter.probes() returns an empty R
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gravatar for Pedro Lopez-Romero
10.5 years ago by
Pedro Lopez-Romero120 wrote:
Hi Massimo, can you show me what you have in targets$Treatment? p.- On Mon, Apr 27, 2009 at 7:17 AM, Massimo Pinto <pintarello@gmail.com> wrote: > I am reposting this only because, from the web archive of this list, it > appears that > An embedded and charset-unspecified text was scrubbed... > Name: not available > > So perhaps my message was never seen on the list, but for those who opt to > receive individual message. Thank you. > Massimo > > ---------- Forwarded message ---------- > From: Massimo Pinto <pintarello@gmail.com> > Date: Fri, Apr 24, 2009 at 6:02 PM > Subject: Agi4x44PreProcess: filtration of probes using filter.probes() > returns an empty RGList. > To: bioconductor@stat.math.ethz.ch > > > Greetings, > on a BioC2.4 installation using with the Agi4x44PreProcess library, I am > trying to invoke the filter.probes() filtration function to remove those > not-so-good probes. > Keeping in mind that my object looks like this: > > dim(ddNORM) > [1] 45015 4 > > class(ddNORM) > [1] "RGList" > attr(,"package") > [1] "limma" > > when I apply the filtration function at the R prompt, using a syntax that I > am copying from the Agi4x44PreProcess manual: > > >ddFILT = filter.probes(ddNORM, control = TRUE, wellaboveBG = TRUE, isfound > = TRUE, wellaboveNEG = TRUE, sat = TRUE, PopnOL = TRUE, NonUnifOL = T, nas > = > TRUE, limWellAbove = 75, limISF = 75, limNEG = 75, limSAT = 75, limPopnOL = > 75, limNonUnifOL = 75, limNAS = 100, makePLOT = TRUE, annotation.package = > "hgug4112a.db", flag.counts = T, targets) > I am getting an empty RGList as output: > FILTERING BY ControlType FLAG > ------------------------------------------------------ > PROBES BEFORE FILTERING: 45015 > PROBES AFTER ControlType FILTERING: 43376 > RAW DATA WITHOUT CONTROLS OUT : 43376 > ------------------------------------------------------ > FILTERING BY IsWellAboveBG filterFLAG > FLAG FILTERING OPTIONS - FLAG OK = 1 - limWellAbove: 75 % > PROBES BEFORE FILTERING: 43376 > PROBES AFTER QC FILTERING: 0 > IsNOTWellAboveBG OUT : 0 > ------------------------------------------------------ > [...] > so it looks to me like filtration by ControlType flag works ok, but > filtration via filter flag IsWellAboveBG returns an empty RGlist, which > remains empty from there onwards, as it seems: > > dim(ddFILT) > [1] 0 4 > However, looking into the variable IsWellAboveBG somewhere in my RGList > ddNORM returns > > ddNORM$other$gIsWellAboveBG[8165:8178,] > 41745_1_3_21 41844_1_2_22 41744_1_2_23 41743_1_3_24 > [1,] 1 1 1 1 > [2,] 1 1 1 1 > [3,] 0 0 0 0 > [4,] 0 0 0 0 > [5,] 1 1 1 1 > [6,] 0 0 0 0 > [7,] 1 1 1 1 > [8,] 1 1 1 1 > [9,] 1 1 1 1 > [10,] 0 0 0 0 > [11,] 0 0 0 0 > [12,] 1 1 1 1 > [13,] 1 1 1 1 > [14,] 1 1 1 1 > > suggesting that, in ddNORM, does have some entries have value 1 for flag > IsWellAboveBG. So why is filter.probes() throwing out all of my data from > ddNORM, assuming none is above background? > I have also tried to suppress filtation by IsWellAboveBG, but the outcome > is > the same upon the next filtration invoked by filter.probes(), i.e. an empty > RGList. > Thank you very much indeed for any clues you may have. Clearly I cannot see > clearly in the use of this function. > Yours > Massimo > > Massimo Pinto > Post Doctoral Research Fellow > Enrico Fermi Centre and Italian Public Health Research Institute (ISS), > Rome > http://claimid.com/massimopinto > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 10.5 years ago by Pedro Lopez-Romero120
Hi again Massimo, please, show me as well what you have in your targets$GErep p.- On Mon, Apr 27, 2009 at 4:01 PM, Pedro Lopez-Romero < plromero1.bioc@gmail.com> wrote: > Hi Massimo, can you show me what you have in targets$Treatment? > > p.- > > On Mon, Apr 27, 2009 at 7:17 AM, Massimo Pinto <pintarello@gmail.com>wrote: > >> I am reposting this only because, from the web archive of this list, it >> appears that >> An embedded and charset-unspecified text was scrubbed... >> Name: not available >> >> So perhaps my message was never seen on the list, but for those who opt to >> receive individual message. Thank you. >> Massimo >> >> ---------- Forwarded message ---------- >> From: Massimo Pinto <pintarello@gmail.com> >> Date: Fri, Apr 24, 2009 at 6:02 PM >> Subject: Agi4x44PreProcess: filtration of probes using filter.probes() >> returns an empty RGList. >> To: bioconductor@stat.math.ethz.ch >> >> >> Greetings, >> on a BioC2.4 installation using with the Agi4x44PreProcess library, I am >> trying to invoke the filter.probes() filtration function to remove those >> not-so-good probes. >> Keeping in mind that my object looks like this: >> > dim(ddNORM) >> [1] 45015 4 >> > class(ddNORM) >> [1] "RGList" >> attr(,"package") >> [1] "limma" >> >> when I apply the filtration function at the R prompt, using a syntax that >> I >> am copying from the Agi4x44PreProcess manual: >> >> >ddFILT = filter.probes(ddNORM, control = TRUE, wellaboveBG = TRUE, >> isfound >> = TRUE, wellaboveNEG = TRUE, sat = TRUE, PopnOL = TRUE, NonUnifOL = T, nas >> = >> TRUE, limWellAbove = 75, limISF = 75, limNEG = 75, limSAT = 75, limPopnOL >> = >> 75, limNonUnifOL = 75, limNAS = 100, makePLOT = TRUE, annotation.package = >> "hgug4112a.db", flag.counts = T, targets) >> I am getting an empty RGList as output: >> FILTERING BY ControlType FLAG >> ------------------------------------------------------ >> PROBES BEFORE FILTERING: 45015 >> PROBES AFTER ControlType FILTERING: 43376 >> RAW DATA WITHOUT CONTROLS OUT : 43376 >> ------------------------------------------------------ >> FILTERING BY IsWellAboveBG filterFLAG >> FLAG FILTERING OPTIONS - FLAG OK = 1 - limWellAbove: 75 % >> PROBES BEFORE FILTERING: 43376 >> PROBES AFTER QC FILTERING: 0 >> IsNOTWellAboveBG OUT : 0 >> ------------------------------------------------------ >> [...] >> so it looks to me like filtration by ControlType flag works ok, but >> filtration via filter flag IsWellAboveBG returns an empty RGlist, which >> remains empty from there onwards, as it seems: >> > dim(ddFILT) >> [1] 0 4 >> However, looking into the variable IsWellAboveBG somewhere in my RGList >> ddNORM returns >> > ddNORM$other$gIsWellAboveBG[8165:8178,] >> 41745_1_3_21 41844_1_2_22 41744_1_2_23 41743_1_3_24 >> [1,] 1 1 1 1 >> [2,] 1 1 1 1 >> [3,] 0 0 0 0 >> [4,] 0 0 0 0 >> [5,] 1 1 1 1 >> [6,] 0 0 0 0 >> [7,] 1 1 1 1 >> [8,] 1 1 1 1 >> [9,] 1 1 1 1 >> [10,] 0 0 0 0 >> [11,] 0 0 0 0 >> [12,] 1 1 1 1 >> [13,] 1 1 1 1 >> [14,] 1 1 1 1 >> >> suggesting that, in ddNORM, does have some entries have value 1 for flag >> IsWellAboveBG. So why is filter.probes() throwing out all of my data from >> ddNORM, assuming none is above background? >> I have also tried to suppress filtation by IsWellAboveBG, but the outcome >> is >> the same upon the next filtration invoked by filter.probes(), i.e. an >> empty >> RGList. >> Thank you very much indeed for any clues you may have. Clearly I cannot >> see >> clearly in the use of this function. >> Yours >> Massimo >> >> Massimo Pinto >> Post Doctoral Research Fellow >> Enrico Fermi Centre and Italian Public Health Research Institute (ISS), >> Rome >> http://claimid.com/massimopinto >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
ADD REPLYlink written 10.5 years ago by Pedro Lopez-Romero120
HI Pedro,thank you. What I am attempting to do here is to find differences in four replicate measurements. Therefore, I defined Biorep for later use in the target file: Target File X FileName Treatment GErep Biorep Culture Array 41745_1_3_21 6moC1Gy1 41745_1_3_21.txt 1Gy 2 1 6moC 41745 41844_1_2_22 6moC1Gy2 41844_1_2_22.txt 1Gy 2 2 6moC 41844 41744_1_2_23 6moC1Gy3 41744_1_2_23.txt 1Gy 2 3 6moC 41744 41743_1_3_24 6moC1Gy4 41743_1_3_24.txt 1Gy 2 4 6moC 41743 On the R console: > targets$Treatment [1] 1Gy 1Gy 1Gy 1Gy Levels: 1Gy > targets$GErep [1] 2 2 2 2 If I add a sample, in my targets, with a different $Treatment, I no longer get the error that I was reporting. Perhaps I a not getting why there should be different treatments in the targets. This works fine: Target File X FileName Treatment GErep Biorep Culture Array 41741_1_1_1 t0Cn 41741_1_1_1.txt Cn 1 1 t0 41741 41745_1_3_21 6moC1Gy1 41745_1_3_21.txt 1Gy 2 1 6moC 41745 41844_1_2_22 6moC1Gy2 41844_1_2_22.txt 1Gy 2 2 6moC 41844 41744_1_2_23 6moC1Gy3 41744_1_2_23.txt 1Gy 2 3 6moC 41744 41743_1_3_24 6moC1Gy4 41743_1_3_24.txt 1Gy 2 4 6moC 41743 Thank you for your insight. Yours Massimo On Mon, Apr 27, 2009 at 10:08 PM, Pedro Lopez-Romero < plromero1.bioc@gmail.com> wrote: > Hi again Massimo, > please, show me as well what you have in your targets$GErep > > p.- > > On Mon, Apr 27, 2009 at 4:01 PM, Pedro Lopez-Romero < > plromero1.bioc@gmail.com> wrote: > >> Hi Massimo, can you show me what you have in targets$Treatment? >> >> p.- >> > -- Massimo Pinto Post Doctoral Research Fellow Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome http://claimid.com/massimopinto [[alternative HTML version deleted]]
ADD REPLYlink written 10.5 years ago by Massimo Pinto390
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