using rma() on XYS files using oligo package
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James Yousin ▴ 30
@james-yousin-6413
Last seen 6.8 years ago
I am trying to do preprocessing on xys files and have used the pdInfoBuilder package to successfully build the annotation files, everything works until rma(), if I skip it I also get the results using ACME. But I would like to know why rma() didnt work with xys files. class(xys) [1] "TilingFeatureSet" attr(,"package") [1] "oligoClasses" rma(xys) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'rma' for signature '"TilingFeatureSet"' is this happening because the object is not of any of the "ExonFeatureSet", "ExpressionFeatureSet", "GeneFeatureSet" or "SnpCnvFeatureSet". I do see elsewhere people got it to work on XYS files https://stat.ethz.ch/pipermail/bioconductor/2013-June/053378.html Thanks James [[alternative HTML version deleted]]
Annotation Preprocessing Annotation Preprocessing • 2.2k views
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@benilton-carvalho-1375
Last seen 14 months ago
Brazil/Campinas/UNICAMP
For tiling arrays, one often prefers to apply a different strategy for preprocessing. But if it's something you really want to do, you can extract the pms and do it "manually": pms = pm(xys) pns = probeNames(xys) res = basicRMA(pms, pns) b 2014-02-19 20:25 GMT-03:00 James Yousin <yousin.james@gmail.com>: > I am trying to do preprocessing on xys files and have used the > pdInfoBuilder package to successfully build the annotation files, > everything works until rma(), if I skip it I also get the results using > ACME. But I would like to know why rma() didnt work with xys files. > > > class(xys) > [1] "TilingFeatureSet" > attr(,"package") > [1] "oligoClasses" > > rma(xys) > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function 'rma' for signature > '"TilingFeatureSet"' > > is this happening because the object is not of any of the "ExonFeatureSet", > "ExpressionFeatureSet", "GeneFeatureSet" or "SnpCnvFeatureSet". > > I do see elsewhere people got it to work on XYS files > > https://stat.ethz.ch/pipermail/bioconductor/2013-June/053378.html > > Thanks > > James > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Thank you a lot for your help. This works. I am trying to perform the ACME after this info <- getNgsColorsInfo(baseDirData, full = TRUE) rawTilingData <- read.xysfiles2(info[,2], info[,1], sampleNames=info[,3]) pms = pm(rawTilingData) pns = probeNames(rawTilingData) res = basicRMA(pms, pns) res2 <- new("TilingFeatureSet", exprs=res) // I think here I am having trouble creating an TilingArray Feature set object, is it possible to create a TilingFeatureSet object after I have performed normalization ? c1 <- channel(res2, "channel1") c2 <- channel(res2, "channel2") On Wed, Feb 19, 2014 at 7:05 PM, Benilton Carvalho < beniltoncarvalho@gmail.com> wrote: > For tiling arrays, one often prefers to apply a different strategy for > preprocessing. > > But if it's something you really want to do, you can extract the pms and > do it "manually": > > pms = pm(xys) > pns = probeNames(xys) > res = basicRMA(pms, pns) > > b > > > 2014-02-19 20:25 GMT-03:00 James Yousin <yousin.james@gmail.com>: > >> I am trying to do preprocessing on xys files and have used the >> pdInfoBuilder package to successfully build the annotation files, >> everything works until rma(), if I skip it I also get the results using >> ACME. But I would like to know why rma() didnt work with xys files. >> >> >> class(xys) >> [1] "TilingFeatureSet" >> attr(,"package") >> [1] "oligoClasses" >> >> rma(xys) >> Error in (function (classes, fdef, mtable) : >> unable to find an inherited method for function 'rma' for signature >> '"TilingFeatureSet"' >> >> is this happening because the object is not of any of the >> "ExonFeatureSet", >> "ExpressionFeatureSet", "GeneFeatureSet" or "SnpCnvFeatureSet". >> >> I do see elsewhere people got it to work on XYS files >> >> https://stat.ethz.ch/pipermail/bioconductor/2013-June/053378.html >> >> Thanks >> >> James >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
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Hi James, please allow me to fix the code I gave you initially. pms = pm(rawTilingData) nc = ncol(pms) pns = probeNames(rawTilingData) res = basicRMA(cbind(pms[,,1], pms[,,2]), pns) res2 = new('NChannelSet', channel1=res[,1:nc], channel2=res[, -c(1:nc)]) the reason I'm suggesting the use of an NChannelSet is because conceptually a 'TilingFeatureSet' is a container for raw data. benilton 2014-02-20 17:46 GMT-03:00 James Yousin <yousin.james@gmail.com>: > > Thank you a lot for your help. This works. > I am trying to perform the ACME after this > > info <- getNgsColorsInfo(baseDirData, full = TRUE) > rawTilingData <- read.xysfiles2(info[,2], info[,1], sampleNames=info[,3]) > > pms = pm(rawTilingData) > pns = probeNames(rawTilingData) > res = basicRMA(pms, pns) > > res2 <- new("TilingFeatureSet", exprs=res) > > // I think here I am having trouble creating an TilingArray Feature set > object, is it possible to create a TilingFeatureSet object after I have > performed normalization ? > > c1 <- channel(res2, "channel1") > c2 <- channel(res2, "channel2") > > > On Wed, Feb 19, 2014 at 7:05 PM, Benilton Carvalho < > beniltoncarvalho@gmail.com> wrote: > >> For tiling arrays, one often prefers to apply a different strategy for >> preprocessing. >> >> But if it's something you really want to do, you can extract the pms and >> do it "manually": >> >> pms = pm(xys) >> pns = probeNames(xys) >> res = basicRMA(pms, pns) >> >> b >> >> >> 2014-02-19 20:25 GMT-03:00 James Yousin <yousin.james@gmail.com>: >> >>> I am trying to do preprocessing on xys files and have used the >>> pdInfoBuilder package to successfully build the annotation files, >>> everything works until rma(), if I skip it I also get the results using >>> ACME. But I would like to know why rma() didnt work with xys files. >>> >>> >>> class(xys) >>> [1] "TilingFeatureSet" >>> attr(,"package") >>> [1] "oligoClasses" >>> >>> rma(xys) >>> Error in (function (classes, fdef, mtable) : >>> unable to find an inherited method for function 'rma' for signature >>> '"TilingFeatureSet"' >>> >>> is this happening because the object is not of any of the >>> "ExonFeatureSet", >>> "ExpressionFeatureSet", "GeneFeatureSet" or "SnpCnvFeatureSet". >>> >>> I do see elsewhere people got it to work on XYS files >>> >>> https://stat.ethz.ch/pipermail/bioconductor/2013-June/053378.html >>> >>> Thanks >>> >>> James >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > [[alternative HTML version deleted]]
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btw, chapter 5 on this old document might be of interest. http://watson.nci.nih.gov/bioc_mirror/packages/2.11/bioc/vignettes/oli go/inst/doc/primer.pdf 2014-02-21 8:19 GMT-03:00 Benilton Carvalho <beniltoncarvalho@gmail.com>: > Hi James, > > please allow me to fix the code I gave you initially. > > pms = pm(rawTilingData) > nc = ncol(pms) > pns = probeNames(rawTilingData) > res = basicRMA(cbind(pms[,,1], pms[,,2]), pns) > res2 = new('NChannelSet', channel1=res[,1:nc], channel2=res[, -c(1:nc)]) > > the reason I'm suggesting the use of an NChannelSet is because > conceptually a 'TilingFeatureSet' is a container for raw data. > > benilton > > > > 2014-02-20 17:46 GMT-03:00 James Yousin <yousin.james@gmail.com>: > > >> Thank you a lot for your help. This works. >> I am trying to perform the ACME after this >> >> info <- getNgsColorsInfo(baseDirData, full = TRUE) >> rawTilingData <- read.xysfiles2(info[,2], info[,1], sampleNames=info[,3]) >> >> pms = pm(rawTilingData) >> pns = probeNames(rawTilingData) >> res = basicRMA(pms, pns) >> >> res2 <- new("TilingFeatureSet", exprs=res) >> >> // I think here I am having trouble creating an TilingArray Feature set >> object, is it possible to create a TilingFeatureSet object after I have >> performed normalization ? >> >> c1 <- channel(res2, "channel1") >> c2 <- channel(res2, "channel2") >> >> >> On Wed, Feb 19, 2014 at 7:05 PM, Benilton Carvalho < >> beniltoncarvalho@gmail.com> wrote: >> >>> For tiling arrays, one often prefers to apply a different strategy for >>> preprocessing. >>> >>> But if it's something you really want to do, you can extract the pms and >>> do it "manually": >>> >>> pms = pm(xys) >>> pns = probeNames(xys) >>> res = basicRMA(pms, pns) >>> >>> b >>> >>> >>> 2014-02-19 20:25 GMT-03:00 James Yousin <yousin.james@gmail.com>: >>> >>>> I am trying to do preprocessing on xys files and have used the >>>> pdInfoBuilder package to successfully build the annotation files, >>>> everything works until rma(), if I skip it I also get the results using >>>> ACME. But I would like to know why rma() didnt work with xys files. >>>> >>>> >>>> class(xys) >>>> [1] "TilingFeatureSet" >>>> attr(,"package") >>>> [1] "oligoClasses" >>>> >>>> rma(xys) >>>> Error in (function (classes, fdef, mtable) : >>>> unable to find an inherited method for function 'rma' for signature >>>> '"TilingFeatureSet"' >>>> >>>> is this happening because the object is not of any of the >>>> "ExonFeatureSet", >>>> "ExpressionFeatureSet", "GeneFeatureSet" or "SnpCnvFeatureSet". >>>> >>>> I do see elsewhere people got it to work on XYS files >>>> >>>> https://stat.ethz.ch/pipermail/bioconductor/2013-June/053378.html >>>> >>>> Thanks >>>> >>>> James >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> >> > [[alternative HTML version deleted]]
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Hello Benilton Thank you again for the updated code I was following the "Supplemental Material: A Framework for Oligonucleotide Microarrays Preprocessing" written by you which I think is same as the document you have linked. http://watson.nci.nih.gov/bioc_mirror/packages/2.11/bioc/vignettes/oli go/inst/doc/primer.pdf the NChannelSet gives error during use of db (SQLite connection to the database), is it because its not any of those supported objects in db ? pms = pm(rawTilingData) nc = ncol(pms) pns = probeNames(rawTilingData) res = basicRMA(cbind(pms[,,1], pms[,,2]), pns) res2 = new('NChannelSet', channel1=res[,1:nc], channel2=res[, -c(1:nc)]) sql <- paste("SELECT fid, fsetid, chrom as chromosome, position as start", "FROM pmfeature INNER JOIN featureSet USING(fsetid)", "ORDER BY chrom, position") annotPM <- dbGetQuery(db(res2), sql) Error in dbGetQuery(db(res2), sql) : error in evaluating the argument 'conn' in selecting a method for function 'dbGetQuery': Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'db' for signature '"NChannelSet" > db(res2) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'db' for signature '"NChannelSet" On Fri, Feb 21, 2014 at 3:21 AM, Benilton Carvalho < beniltoncarvalho@gmail.com> wrote: > btw, chapter 5 on this old document might be of interest. > > > http://watson.nci.nih.gov/bioc_mirror/packages/2.11/bioc/vignettes/o ligo/inst/doc/primer.pdf > > > 2014-02-21 8:19 GMT-03:00 Benilton Carvalho <beniltoncarvalho@gmail.com>: > > Hi James, >> >> please allow me to fix the code I gave you initially. >> >> pms = pm(rawTilingData) >> nc = ncol(pms) >> pns = probeNames(rawTilingData) >> res = basicRMA(cbind(pms[,,1], pms[,,2]), pns) >> res2 = new('NChannelSet', channel1=res[,1:nc], channel2=res[, -c(1:nc)]) >> >> the reason I'm suggesting the use of an NChannelSet is because >> conceptually a 'TilingFeatureSet' is a container for raw data. >> >> benilton >> >> >> >> 2014-02-20 17:46 GMT-03:00 James Yousin <yousin.james@gmail.com>: >> >> >>> Thank you a lot for your help. This works. >>> I am trying to perform the ACME after this >>> >>> info <- getNgsColorsInfo(baseDirData, full = TRUE) >>> rawTilingData <- read.xysfiles2(info[,2], info[,1], sampleNames=info[,3]) >>> >>> pms = pm(rawTilingData) >>> pns = probeNames(rawTilingData) >>> res = basicRMA(pms, pns) >>> >>> res2 <- new("TilingFeatureSet", exprs=res) >>> >>> // I think here I am having trouble creating an TilingArray Feature set >>> object, is it possible to create a TilingFeatureSet object after I have >>> performed normalization ? >>> >>> c1 <- channel(res2, "channel1") >>> c2 <- channel(res2, "channel2") >>> >>> >>> On Wed, Feb 19, 2014 at 7:05 PM, Benilton Carvalho < >>> beniltoncarvalho@gmail.com> wrote: >>> >>>> For tiling arrays, one often prefers to apply a different strategy for >>>> preprocessing. >>>> >>>> But if it's something you really want to do, you can extract the pms >>>> and do it "manually": >>>> >>>> pms = pm(xys) >>>> pns = probeNames(xys) >>>> res = basicRMA(pms, pns) >>>> >>>> b >>>> >>>> >>>> 2014-02-19 20:25 GMT-03:00 James Yousin <yousin.james@gmail.com>: >>>> >>>>> I am trying to do preprocessing on xys files and have used the >>>>> pdInfoBuilder package to successfully build the annotation files, >>>>> everything works until rma(), if I skip it I also get the results using >>>>> ACME. But I would like to know why rma() didnt work with xys files. >>>>> >>>>> >>>>> class(xys) >>>>> [1] "TilingFeatureSet" >>>>> attr(,"package") >>>>> [1] "oligoClasses" >>>>> >>>>> rma(xys) >>>>> Error in (function (classes, fdef, mtable) : >>>>> unable to find an inherited method for function 'rma' for signature >>>>> '"TilingFeatureSet"' >>>>> >>>>> is this happening because the object is not of any of the >>>>> "ExonFeatureSet", >>>>> "ExpressionFeatureSet", "GeneFeatureSet" or "SnpCnvFeatureSet". >>>>> >>>>> I do see elsewhere people got it to work on XYS files >>>>> >>>>> https://stat.ethz.ch/pipermail/bioconductor/2013-June/053378.html >>>>> >>>>> Thanks >>>>> >>>>> James >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>> >>>> >>> >> > [[alternative HTML version deleted]]
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Hi James, on that document, RMA isn't mentioned for tiling arrays. The dbGetQuery() you're referring to is actually performed on the rawTilingData object. If you must run RMA, then you want to redefine your dbGetQuery call. Maybe something along the lines of: pms = pm(rawTilingData) nc = ncol(pms) pns = probeNames(rawTilingData) res = basicRMA(cbind(pms[,,1], pms[,,2]), pns) channel1 = res[, 1:nc] channel2 = res[, -c(1:nc)] conn = db(rawTilingData) sql = 'SELECT man_fsetid, chrom, start, end FROM featureSet WHERE man_fsetid = :name' info = dbGetPreparedQuery(conn, sql, data.frame(name=rownames(res))) idx = with(info, order(chrom, start)) info = info[idx,] res = res[idx,] channel1 = channel1[idx,] channel2 = channel2[idx,] logR = channel1 - channel2 HTH, b 2014-02-24 19:15 GMT-03:00 James Yousin <yousin.james@gmail.com>: > Hello Benilton > > Thank you again for the updated code > I was following the "Supplemental Material: A Framework for > Oligonucleotide Microarrays Preprocessing" written by you which I think is > same as > the document you have linked. > > http://watson.nci.nih.gov/bioc_mirror/packages/2.11/bioc/vignettes/o ligo/inst/doc/primer.pdf > > the NChannelSet gives error during use of db (SQLite connection to the > database), is it because its not any of those supported objects in db ? > > pms = pm(rawTilingData) > nc = ncol(pms) > pns = probeNames(rawTilingData) > res = basicRMA(cbind(pms[,,1], pms[,,2]), pns) > res2 = new('NChannelSet', channel1=res[,1:nc], channel2=res[, -c(1:nc)]) > sql <- paste("SELECT fid, fsetid, chrom as chromosome, position as start", > "FROM pmfeature INNER JOIN featureSet USING(fsetid)", > "ORDER BY chrom, position") > annotPM <- dbGetQuery(db(res2), sql) > Error in dbGetQuery(db(res2), sql) : > error in evaluating the argument 'conn' in selecting a method for > function 'dbGetQuery': Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function 'db' for signature > '"NChannelSet" > > > db(res2) > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function 'db' for signature > '"NChannelSet" > > > > > On Fri, Feb 21, 2014 at 3:21 AM, Benilton Carvalho < > beniltoncarvalho@gmail.com> wrote: > >> btw, chapter 5 on this old document might be of interest. >> >> >> http://watson.nci.nih.gov/bioc_mirror/packages/2.11/bioc/vignettes/ oligo/inst/doc/primer.pdf >> >> >> 2014-02-21 8:19 GMT-03:00 Benilton Carvalho <beniltoncarvalho@gmail.com>: >> >> Hi James, >>> >>> please allow me to fix the code I gave you initially. >>> >>> pms = pm(rawTilingData) >>> nc = ncol(pms) >>> pns = probeNames(rawTilingData) >>> res = basicRMA(cbind(pms[,,1], pms[,,2]), pns) >>> res2 = new('NChannelSet', channel1=res[,1:nc], channel2=res[, -c(1:nc)]) >>> >>> the reason I'm suggesting the use of an NChannelSet is because >>> conceptually a 'TilingFeatureSet' is a container for raw data. >>> >>> benilton >>> >>> >>> >>> 2014-02-20 17:46 GMT-03:00 James Yousin <yousin.james@gmail.com>: >>> >>> >>>> Thank you a lot for your help. This works. >>>> I am trying to perform the ACME after this >>>> >>>> info <- getNgsColorsInfo(baseDirData, full = TRUE) >>>> rawTilingData <- read.xysfiles2(info[,2], info[,1], >>>> sampleNames=info[,3]) >>>> >>>> pms = pm(rawTilingData) >>>> pns = probeNames(rawTilingData) >>>> res = basicRMA(pms, pns) >>>> >>>> res2 <- new("TilingFeatureSet", exprs=res) >>>> >>>> // I think here I am having trouble creating an TilingArray Feature set >>>> object, is it possible to create a TilingFeatureSet object after I have >>>> performed normalization ? >>>> >>>> c1 <- channel(res2, "channel1") >>>> c2 <- channel(res2, "channel2") >>>> >>>> >>>> On Wed, Feb 19, 2014 at 7:05 PM, Benilton Carvalho < >>>> beniltoncarvalho@gmail.com> wrote: >>>> >>>>> For tiling arrays, one often prefers to apply a different strategy for >>>>> preprocessing. >>>>> >>>>> But if it's something you really want to do, you can extract the pms >>>>> and do it "manually": >>>>> >>>>> pms = pm(xys) >>>>> pns = probeNames(xys) >>>>> res = basicRMA(pms, pns) >>>>> >>>>> b >>>>> >>>>> >>>>> 2014-02-19 20:25 GMT-03:00 James Yousin <yousin.james@gmail.com>: >>>>> >>>>>> I am trying to do preprocessing on xys files and have used the >>>>>> pdInfoBuilder package to successfully build the annotation files, >>>>>> everything works until rma(), if I skip it I also get the results >>>>>> using >>>>>> ACME. But I would like to know why rma() didnt work with xys files. >>>>>> >>>>>> >>>>>> class(xys) >>>>>> [1] "TilingFeatureSet" >>>>>> attr(,"package") >>>>>> [1] "oligoClasses" >>>>>> >>>>>> rma(xys) >>>>>> Error in (function (classes, fdef, mtable) : >>>>>> unable to find an inherited method for function 'rma' for signature >>>>>> '"TilingFeatureSet"' >>>>>> >>>>>> is this happening because the object is not of any of the >>>>>> "ExonFeatureSet", >>>>>> "ExpressionFeatureSet", "GeneFeatureSet" or "SnpCnvFeatureSet". >>>>>> >>>>>> I do see elsewhere people got it to work on XYS files >>>>>> >>>>>> https://stat.ethz.ch/pipermail/bioconductor/2013-June/053378.html >>>>>> >>>>>> Thanks >>>>>> >>>>>> James >>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor@r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>> >>>>> >>>> >>> >> > [[alternative HTML version deleted]]
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