regarding GCRMA normalization

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sneha patil ▴ 220

@sneha-patil-3903

Last seen 9.6 years ago

hiii, i have prepared the HuGene-1_0-st-v1.r3.cdf package...and want to preapare a probe package....while making the probe package i am getting this error.....also my probe file is the zip file.,.... > makeProbePackage("Hugene-1_0-st-v1.r3",datafile = gzfile("HuGene-1_0-st-v1.probe.tab",open="r"), + outdir = "outdir",maintainer = "me",version = "0.0.1",species = "Homo_sapiens", + check = FALSE,force = TRUE) Importing the data. Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'an integer', got '+' plzz help me regarding this [[alternative HTML version deleted]]

cdf probe cdf probe • 1.0k views

ADD COMMENT • link 14.2 years ago sneha patil ▴ 220

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sneha patil ▴ 220

@sneha-patil-3903

Last seen 9.6 years ago

hiii, i have created the cdf package but while creating the probe package i am getting this error...please help me out... > makeProbePackage("hugene10stv1.r3cdf",datafile=gzfile("HuGene- 1_0-st-v1.probe.tab.gz", + open = "r"),outdir = "outdir",maintainer ="me",version = "0.0.1",force = TRUE) Error in makeProbePackage("hugene10stv1.r3cdf", datafile = gzfile("HuGene-1_0-st-v1.probe.tab.gz", : 'species' is missing or invalid. Please specify the species that the package will pertain to using the form: Genus_species (e.g., Homo_sapiens). [[alternative HTML version deleted]]

ADD COMMENT • link 14.2 years ago sneha patil ▴ 220

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 15 hours ago

United States

Hi Sneha, There are going to be several problems for you. First, the getDataAffy() function expects the data to be in a certain format which is obviously being violated here. So you _could_ modify the probe_tab file to conform to that format. However, a bigger problem is that the chip you are using is a PM-only chip. There are some background probes on the chip, but they are not MM-probes so I don't believe the underlying assumptions for the gcrma model are going to apply. Best, Jim James W. MacDonald, M.S. Biostatistician Douglas Lab 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 >>> sneha patil 01/28/10 2:04 AM >>> hiii, i have prepared the HuGene-1_0-st-v1.r3.cdf package...and want to preapare a probe package....while making the probe package i am getting this error.....also my probe file is the zip file.,.... > makeProbePackage("Hugene-1_0-st-v1.r3",datafile = gzfile("HuGene-1_0-st-v1.probe.tab",open="r"), + outdir = "outdir",maintainer = "me",version = "0.0.1",species = "Homo_sapiens", + check = FALSE,force = TRUE) Importing the data. Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'an integer', got '+' plzz help me regarding this [[alternative HTML version deleted]] _______________________________________________ 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

ADD COMMENT • link 14.2 years ago James W. MacDonald 65k

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We are still in the process of implementing GCRMA for the gene ST platforms and it is not yet included in the current version. Best, Jean Wu James MacDonald wrote: > Hi Sneha, > > There are going to be several problems for you. First, the getDataAffy() function expects the data to be in a certain format which is obviously being violated here. So you _could_ modify the probe_tab file to conform to that format. > > However, a bigger problem is that the chip you are using is a PM- only chip. There are some background probes on the chip, but they are not MM-probes so I don't believe the underlying assumptions for the gcrma model are going to apply. > > Best, > > Jim > > > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 >>>> sneha patil 01/28/10 2:04 AM >>> > hiii, > > i have prepared the HuGene-1_0-st-v1.r3.cdf package...and want to preapare a > probe package....while making the probe package i am getting this > error.....also my probe file is the zip file.,.... > >> makeProbePackage("Hugene-1_0-st-v1.r3",datafile = > gzfile("HuGene-1_0-st-v1.probe.tab",open="r"), > + outdir = "outdir",maintainer = "me",version = "0.0.1",species = > "Homo_sapiens", > + check = FALSE,force = TRUE) > Importing the data. > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, > : > scan() expected 'an integer', got '+' > > > plzz help me regarding this > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues > > _______________________________________________ > 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 -- ------------------------------------ Zhijin (Jean) Wu Assistant Professor of Biostatistics Brown University, Box G-S121 Providence, RI 02912 Tel: 401 863 1230 Fax: 401 863 9182 http://www.stat.brown.edu/zwu

ADD REPLY • link 14.2 years ago Zhijin Wu ▴ 260

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sneha patil ▴ 220

@sneha-patil-3903

Last seen 9.6 years ago

hiii, i have prepared the HuGene-1_0-st-v1.r3.cdf package...and want to preapare a probe package....while making the probe package i am getting this error.....also my probe file is the zip file.,.... > makeProbePackage("Hugene-1_0-st-v1.r3",datafile = gzfile("HuGene-1_0-st-v1.probe.tab",open="r"), + outdir = "outdir",maintainer = "me",version = "0.0.1",species = "Homo_sapiens", + check = FALSE,force = TRUE) Importing the data. Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'an integer', got '+' following is the session info and traceback > sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.24.2 matchprobes_1.18.0 Biostrings_2.14.10 [4] IRanges_1.4.10 AnnotationDbi_1.8.1 makecdfenv_1.25.1 [7] Biobase_2.6.1 loaded via a namespace (and not attached): [1] affyio_1.14.0 DBI_0.2-5 preprocessCore_1.8.0 [4] RSQLite_0.8-1 tools_2.10.1 > traceback() 4: scan(datafile, sep = "\t", quiet = TRUE, multi.line = FALSE, what = what) 3: getProbeDataAffy(arraytype = "Hugene-1_0-st-v1.r3", datafile = 4L) 2: do.call(importfun, c(arraytype = arraytype, pkgname = pkgname, list(...))) 1: makeProbePackage("Hugene-1_0-st-v1.r3", datafile = gzfile("HuGene-1_0-st-v1.probe.tab", open = "r"), outdir = "outdir", maintainer = "me", version = "0.0.1", species = "Homo_sapiens", check = FALSE, force = TRUE) plzz help me regarding this [[alternative HTML version deleted]]

ADD COMMENT • link 14.2 years ago sneha patil ▴ 220

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