modify CDF file for array study
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Hyuna Yang ▴ 10
@hyuna-yang-2463
Last seen 9.6 years ago
Dear All, I am using affy array, and want to modify CDF file. For example, instead of all probes in a probe set, I want to use some of them. My naive approach was, read data files modify them, replace the original data, and remake a package, install the modified package, and following shows specifically what I did. I am using brainarray CDF, but guess this does not matter. To use this CDF I need 'mma2mmentrezgprobe' (containing map) and 'mma2mmentrezgcdf'(location of each probeset). i) I read the 'mma2mmentrezgprobe' under the mma2mmentrezgprobe/data and remove some rows (mma2mmentrezgprobe = mma2mmentrezgprobe[-c(1:2),], and save it under the original directory (save(mma2mmentrezgprobem, file='mma2mmentrezgprobe/data/mma2mmentrezgprobe.rda')) ii) remove corresponding rows in data ('mma2mmentrezgcdf') under mma2mmentrezgcdf/data using assign and get; something like this b = get(ls(mma2mmentrezgcdf)[1], mma2mmentrezgcdf) ; b = b[-1:2,] ; assign(ls(mma2mmentrezgcdf)[1], b, envir = mma2mmentrezgcdf) ; #then save this; save(mma2mmentrezgcdf, file = ''mma2mmentrezgcdf/data/mma2mmentrezgcdf') then make a package and install it again. (R CMD build mma2mmentrezgcdf; R CMD INSTALL mma2mmentrezgcdf;) However, it does not work. It seems has problem in ".next.method(e1, e2)" I wonder if someone can help me to modify existing CDF file. Thanks you, Hyuna
cdf probe affy ASSIGN cdf probe affy ASSIGN • 751 views
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Guido Hooiveld ★ 3.9k
@guido-hooiveld-2020
Last seen 1 day ago
Wageningen University, Wageningen, the …
Hi Hyuna, I don't have experience with removing (masking) individual probes from a probeset, but I have used the procedure described in the thread linked to below to remove complete probesets from a CDF file. However, it is mentioned that "listOutProbes" could be used to remove probes. HTH, Guido http://article.gmane.org/gmane.science.biology.informatics.conductor/9 86 9 ### The first part is just creating two ojects (ResetEnvir and RemoveProbes) originally ### written by Ariel Chernomoretz and modified by Jenny Drnevich to remove individual ### probes and/or entire probesets. ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com email: guido.hooiveld at wur.nl > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Hyuna Yang > Sent: 30 October 2007 16:56 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] modify CDF file for array study > > Dear All, > > I am using affy array, and want to modify CDF file. For > example, instead of all probes in a probe set, I want to use > some of them. > My naive approach was, read data files modify them, replace > the original data, and remake a package, install the modified > package, and following shows specifically what I did. > > I am using brainarray CDF, but guess this does not matter. To > use this CDF I need 'mma2mmentrezgprobe' (containing map) and > 'mma2mmentrezgcdf'(location of each probeset). > > i) I read the 'mma2mmentrezgprobe' under the > mma2mmentrezgprobe/data and remove some rows > (mma2mmentrezgprobe = mma2mmentrezgprobe[-c(1:2),], and save > it under the original directory (save(mma2mmentrezgprobem, > file='mma2mmentrezgprobe/data/mma2mmentrezgprobe.rda')) > > ii) remove corresponding rows in data ('mma2mmentrezgcdf') > under mma2mmentrezgcdf/data using assign and get; something > like this b = get(ls(mma2mmentrezgcdf)[1], mma2mmentrezgcdf) > ; b = b[-1:2,] ; assign(ls(mma2mmentrezgcdf)[1], b, envir = > mma2mmentrezgcdf) ; #then save this; save(mma2mmentrezgcdf, > file = ''mma2mmentrezgcdf/data/mma2mmentrezgcdf') > > then make a package and install it again. > (R CMD build mma2mmentrezgcdf; R CMD INSTALL mma2mmentrezgcdf;) > > However, it does not work. It seems has problem in > ".next.method(e1, e2)" > > I wonder if someone can help me to modify existing CDF file. > > Thanks you, > > > Hyuna > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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@michal-okoniewski-1752
Last seen 9.6 years ago
Hi Hyuna, You can modify CDF to do experiments "on the fly" without creating a metadata library. CDF is just an environment. So: 1) get the pre-installed CDF as an environment, eg: library("exon.pmcdf") my.env <- get("exon.pmcdf") 2) attach the CDF to your AffyBatch: raw.data at cdfName <- "exon.pmcdf" 3) Modify the CDF as you wish. it consists of variables with names identical to probesets and the values are data frame with "pm" and "mm" columns. So you can do, eg: assign("2315108",rbind(get("2315108", envir=my.env),get("2315108", envir=my.env)),env=my.env) This example merges probes from two probesets into one. You can use get(), assign(), rm() etc to play around with the CDF environment. 4) Run the summarization and interpret it according to your beliefs and intuitions ;) 5) Once you are happy with the CDF environment you may save it for good using makecdfenv package. Have fun, Michal -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Hyuna Yang Sent: 30 October 2007 15:56 To: bioconductor at stat.math.ethz.ch Subject: [BioC] modify CDF file for array study Dear All, I am using affy array, and want to modify CDF file. For example, instead of all probes in a probe set, I want to use some of them. My naive approach was, read data files modify them, replace the original data, and remake a package, install the modified package, and following shows specifically what I did. I am using brainarray CDF, but guess this does not matter. To use this CDF I need 'mma2mmentrezgprobe' (containing map) and 'mma2mmentrezgcdf'(location of each probeset). i) I read the 'mma2mmentrezgprobe' under the mma2mmentrezgprobe/data and remove some rows (mma2mmentrezgprobe = mma2mmentrezgprobe[-c(1:2),], and save it under the original directory (save(mma2mmentrezgprobem, file='mma2mmentrezgprobe/data/mma2mmentrezgprobe.rda')) ii) remove corresponding rows in data ('mma2mmentrezgcdf') under mma2mmentrezgcdf/data using assign and get; something like this b = get(ls(mma2mmentrezgcdf)[1], mma2mmentrezgcdf) ; b = b[-1:2,] ; assign(ls(mma2mmentrezgcdf)[1], b, envir = mma2mmentrezgcdf) ; #then save this; save(mma2mmentrezgcdf, file = ''mma2mmentrezgcdf/data/mma2mmentrezgcdf') then make a package and install it again. (R CMD build mma2mmentrezgcdf; R CMD INSTALL mma2mmentrezgcdf;) However, it does not work. It seems has problem in ".next.method(e1, e2)" I wonder if someone can help me to modify existing CDF file. Thanks you, Hyuna _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:13}}
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