PreProcess and Limma 'done'. What directions now?
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Massimo Pinto ▴ 390
@massimo-pinto-3396
Last seen 6.6 years ago
Greetings BioC list readers, I have been working over the past few weeks on data normalization first (Agi4X44PreProcess) and linear models then (limma). I sense that I may have reached a point where questions may be addressed regarding regulation of individual genes of interest, as well as gene ontology. Would you please so kindly provide advice with regards to my next step? In brief, I would like to 1) Query expression of genes of my interest, which are known to be implicated in the biology that I am working on 2) Get information about gene ontology 3) Ask about involvement of signaling pahways May be that the goProfiles manual is my next trail? Thank you in advance, Massimo -- Massimo Pinto Post Doctoral Research Fellow Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome http://claimid.com/massimopinto
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@steve-lianoglou-2771
Last seen 3 days ago
Denali
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Hi Massimo >I have beem through normalization and basic limma operations. Does this mean you have extracted lists of genes using topTable? You can add your annotation to these lists of genes using the "genelist" parameter of topTable. Something like "genelist=cbind(fit$genes, mappings)". Assuming your mappings are in the same order as your fit data. >What I would like to do here is to ask questions like "what happened to this >and that particular gene"? You can extract any gene you like from a topTable gene list. Along with the expression/p-values etc. You can extract the actual expression values using the Affymetrix probe name or your gene annotation name. > in place of their Agilent Probe ID. Should be > possible, since I have an annotation file. Yes. Regards John ADD REPLY 0 Entering edit mode Hi John, On Wed, Jun 10, 2009 at 12:15 PM, john seers (IFR)<john.seers at="" bbsrc.ac.uk=""> wrote: > > Hi Massimo > >>I have beem through normalization and basic limma operations. > > Does this mean you have extracted lists of genes using topTable? You can > add your annotation to these lists of genes using the "genelist" > parameter of topTable. Something like "genelist=cbind(fit$genes, > mappings)". Assuming your mappings are in the same order as your fit > data. > yes they seem so > fit2.Cn.eb$genes[1:10,1] [1] "A_24_P66027" "A_32_P77178" "A_23_P212522" "A_24_P934473" "A_24_P9671" "A_24_P801451" "A_32_P30710" "A_24_P704878" "A_32_P86028" [10] "A_23_P65830" > mappings[1:10,1] [1] A_24_P66027 A_32_P77178 A_23_P212522 A_24_P934473 A_24_P9671 A_24_P801451 A_32_P30710 A_24_P704878 A_32_P86028 A_23_P65830 25574 Levels: A_23_P100001 A_23_P100011 A_23_P100022 A_23_P100074 A_23_P100092 A_23_P100103 A_23_P100111 A_23_P100127 ... A_32_P99933 therefore using your suggestion, topTable() nicely returns > toptable(fit2.Cn.eb,genelist=cbind(mappings$DESCRIPTION, fit2.Cn.eb$genes), number=5) mappings.DESCRIPTION ID logFC t P.Value adj.P.Val B 14442 fatty acid binding protein 4, adipocyte A_23_P8812 -3.055038 -17.02303 7.819269e-14 1.999700e-09 18.06843 15172 beta-site APP-cleaving enzyme 2 A_24_P14584 -2.287226 -15.25732 6.721762e-13 6.639688e-09 16.72509 8406 hypothetical protein MGC10981 A_32_P178092 -1.899104 -15.14233 7.788795e-13 6.639688e-09 16.62917 3390 beta-site APP-cleaving enzyme 2 A_23_P154875 -2.006084 -14.41987 2.009131e-12 1.284538e-08 16.00055 4688 forkhead box N3 A_23_P140405 -1.175783 -13.22849 1.047477e-11 5.357635e-08 14.85805 >>What I would like to do here is to ask questions like "what happened to > this >>and that particular gene"? > > You can extract any gene you like from a topTable gene list. Along with > the expression/p-values etc. You can extract the actual expression > values using the Affymetrix probe name or your gene annotation name. > to tackle this I will look more closely into the suggestion written by Vincent (whom I would like to thank here, for a start). Thanks to you too. Massimo [...] ADD REPLY 0 Entering edit mode Hello John On Wed, Jun 10, 2009 at 12:15 PM, john seers (IFR)<john.seers at="" bbsrc.ac.uk=""> wrote: > > Hi Massimo > >>I have beem through normalization and basic limma operations. > > Does this mean you have extracted lists of genes using topTable? You can > add your annotation to these lists of genes using the "genelist" > parameter of topTable. Something like "genelist=cbind(fit$genes, > mappings)". Assuming your mappings are in the same order as your fit > data. > >>What I would like to do here is to ask questions like "what happened to > this >>and that particular gene"? > > You can extract any gene you like from a topTable gene list. Along with > the expression/p-values etc. You can extract the actual expression > values using the Affymetrix probe name or your gene annotation name. > I have played around with topTable() and topTableF() and I am getting to knowing it better now. However, I am missing the point you are making here above. I cannot see how do you pass topTable() info with regards to which genes or which set of genes you wish to know about. I am assuming that topTable() was designed for this purpose, but since this is coming towards interrogating user-specified sets of genes, I may be wrong. Cheers Massimo
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Hi Massimo You are probably reading too much into what I said. I was just trying to say to you that you can combine your annotation information with the Affymetrix probes and the limma output. And Vincent gave you information on how you can search the annotation data. >>What I would like to do here is to ask questions like "what happened to this >>and that particular gene"? Without this question being more definite it is not easy to predict what you need to do. What I was saying is you can search on your expression values by Affymetrix probe (or Annotation id), or on your toptables, to extract any gene or genes of interest. That defines what has happened to this and that particular gene. What you want to do further is an open question. Are you asking how to search for a gene in a toptable? Something like: geneofinterest<-"myaffymetrixprobe" myrows<-which(mytoptable[, "correctcolumnname"] == geneofinterest) mygeneofinterest<-mytoptable[myrows,] Sorry if I do not understand what you need to know. Regards John -----Original Message----- From: Massimo Pinto [mailto:pintarello@gmail.com] Sent: 11 June 2009 11:29 To: john seers (IFR) Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] PreProcess and Limma 'done'. What directions now? Hello John On Wed, Jun 10, 2009 at 12:15 PM, john seers (IFR)<john.seers at="" bbsrc.ac.uk=""> wrote: > > Hi Massimo > >>I have beem through normalization and basic limma operations. > > Does this mean you have extracted lists of genes using topTable? You can > add your annotation to these lists of genes using the "genelist" > parameter of topTable. Something like "genelist=cbind(fit$genes, > mappings)". Assuming your mappings are in the same order as your fit > data. > >>What I would like to do here is to ask questions like "what happened to > this >>and that particular gene"? > > You can extract any gene you like from a topTable gene list. Along with > the expression/p-values etc. You can extract the actual expression > values using the Affymetrix probe name or your gene annotation name. > I have played around with topTable() and topTableF() and I am getting to knowing it better now. However, I am missing the point you are making here above. I cannot see how do you pass topTable() info with regards to which genes or which set of genes you wish to know about. I am assuming that topTable() was designed for this purpose, but since this is coming towards interrogating user-specified sets of genes, I may be wrong. Cheers Massimo ADD REPLY 0 Entering edit mode John, you ended up getting very close to were I needed to be. To compare microarray results to previous data which I had got using other techniques to measure gene expression, I was asked by a colleague to report the micraorray expression levels of selected genes of our interest. much inspired by what you did, I proceed as follows: First I created a vector of probeID: > GOI.redox # vector of genes of interest in the context: redox [1] "A_23_P150281" "A_24_P89457" "A_23_P3038" "A_23_P133474" "A_23_P28075" "A_23_P214544" "A_23_P250671" "A_32_P78121" "A_23_P154840" # "A_23_P105138" then, for a given topTable such as > t0Cn.Vs.6moACn.topTable <- topTable(fit2.Cn.eb, coef=1, genelist=cbind(mappings$DESCRIPTION, fit2.Cn.eb$genes), number=Inf, adjust="BH") I defined a loop to find where all those probes are in the topTable >for (i in 0:length(GOI.redox)) { + myrows[i] <- which(t0Cn.Vs.6moACn.topTable[, "ID"] == GOI.redox[i]) + } > t0Cn.Vs.6moACn.topTable[myrows,] # outputs a specified portion of your topTable with the genes that you wanted. that does it. May be not the most elegant syntax, as I suppose one may well do without a loop, but it does just what I need to show my colleague. Cheers, once again! Massimo On Thu, Jun 11, 2009 at 1:02 PM, john seers (IFR)<john.seers at="" bbsrc.ac.uk=""> wrote: > > Hi Massimo > > You are probably reading too much into what I said. I was just trying to > say to you that you can combine your annotation information with the > Affymetrix probes and the limma output. And Vincent gave you information > on how you can search the annotation data. > >>>What I would like to do here is to ask questions like "what happened > to this >>>and that particular gene"? > > Without this question being more definite it is not easy to predict what > you need to do. What I was saying is you can search on your expression > values by Affymetrix probe (or Annotation id), or on your toptables, to > extract any gene or genes of interest. That defines what has happened to > this and that particular gene. What you want to do further is an open > question. > > Are you asking how to search for a gene in a toptable? Something like: > > geneofinterest<-"myaffymetrixprobe" > myrows<-which(mytoptable[, "correctcolumnname"] == geneofinterest) > mygeneofinterest<-mytoptable[myrows,] > > > Sorry if I do not understand what you need to know. > > Regards > > John > > > > > -----Original Message----- > From: Massimo Pinto [mailto:pintarello at gmail.com] > Sent: 11 June 2009 11:29 > To: john seers (IFR) > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] PreProcess and Limma 'done'. What directions now? > > Hello John > > On Wed, Jun 10, 2009 at 12:15 PM, john seers > (IFR)<john.seers at="" bbsrc.ac.uk=""> wrote: >> >> Hi Massimo >> >>>I have beem through normalization and basic limma operations. >> >> Does this mean you have extracted lists of genes using topTable? You > can >> add your annotation to these lists of genes using the "genelist" >> parameter of topTable. Something like "genelist=cbind(fit$genes, >> mappings)". Assuming your mappings are in the same order as your fit >> data. >> >>>What I would like to do here is to ask questions like "what happened > to >> this >>>and that particular gene"? >> >> You can extract any gene you like from a topTable gene list. Along > with >> the expression/p-values etc. You can extract the actual expression >> values using the Affymetrix probe name or your gene annotation name. >> > > I have played around with topTable() and topTableF() and I am getting > to knowing it better now. However, I am missing the point you are > making here above. I cannot see how do you pass topTable() info with > regards to which genes or which set of genes you wish to know about. > > I am assuming that topTable() was designed for this purpose, but since > this is coming towards interrogating user-specified sets of genes, I > may be wrong. > > Cheers > Massimo > -- Massimo Pinto Post Doctoral Research Fellow Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome http://claimid.com/massimopinto