u133aaofav2
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Simens Zhong ▴ 20
@simens-zhong-2426
Last seen 7.3 years ago
Hi, all, I got problems when normalizing HT-HG_U133A Early Access Array. What I did is as follows, library(u133aaofav2cdf) library(affy) library(gcrma) Data <- ReadAffy() tmp <- gcrma(Data) Adjusting for optical effect.................................................... ...................................................................... ........Do ne. Computing affinities[1] "Checking to see if your internet connection works..." [1] "Environment u133aaofav2probe was not found in the Bioconductor repository." Error in get(x, envir, mode, inherits) : variable "u133aaofav2probe" was not fou nd Execution halted I did find the package "u133aaofav2cdf", but "u133aaofav2probe" seems to me unavailable in bioconductor. has any idea? Thanks. SZ
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@james-w-macdonald-5106
Last seen 1 day ago
United States
Hi Simens, As far as I know, there isn't a probe file available for this particular chip. If you can tell me where I can download one, I am happy to make a probe package and then we will make it available via biocLite(). Best, Jim Simens Zhong wrote: > Hi, all, > > > I got problems when normalizing HT-HG_U133A Early Access Array. What I did > is as follows, > > library(u133aaofav2cdf) > library(affy) > library(gcrma) > > Data <- ReadAffy() > tmp <- gcrma(Data) > Adjusting for optical > effect.................................................... > .................................................................... ..........Do > ne. > Computing affinities[1] "Checking to see if your internet connection > works..." > [1] "Environment u133aaofav2probe was not found in the Bioconductor > repository." > Error in get(x, envir, mode, inherits) : variable "u133aaofav2probe" was > not fou > nd > Execution halted > > > I did find the package "u133aaofav2cdf", but "u133aaofav2probe" seems to > me unavailable in bioconductor. has any idea? > > Thanks. > > SZ > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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The data link is as follows, http://www.ebi.ac.uk/microarray-as/aer/jsp/ae-view- experiment.jsp?accnum=E-TABM-158 The Pubmed ID of this study is 17157792. Thanks, SZ > Hi Simens, > > As far as I know, there isn't a probe file available for this particular > chip. If you can tell me where I can download one, I am happy to make a > probe package and then we will make it available via biocLite(). > > Best, > > Jim > > > > Simens Zhong wrote: >> Hi, all, >> >> >> I got problems when normalizing HT-HG_U133A Early Access Array. What I >> did >> is as follows, >> >> library(u133aaofav2cdf) >> library(affy) >> library(gcrma) >> >> Data <- ReadAffy() >> tmp <- gcrma(Data) >> Adjusting for optical >> effect.................................................... >> ................................................................... ...........Do >> ne. >> Computing affinities[1] "Checking to see if your internet connection >> works..." >> [1] "Environment u133aaofav2probe was not found in the Bioconductor >> repository." >> Error in get(x, envir, mode, inherits) : variable "u133aaofav2probe" was >> not fou >> nd >> Execution halted >> >> >> I did find the package "u133aaofav2cdf", but "u133aaofav2probe" seems to >> me unavailable in bioconductor. has any idea? >> >> Thanks. >> >> SZ >> >> _______________________________________________ >> 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 > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 >
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I don't see a link to a probe file there. Simens Zhong wrote: > The data link is as follows, > > http://www.ebi.ac.uk/microarray-as/aer/jsp/ae-view- experiment.jsp?accnum=E-TABM-158 > > The Pubmed ID of this study is 17157792. > > Thanks, > > SZ > > >> Hi Simens, >> >> As far as I know, there isn't a probe file available for this particular >> chip. If you can tell me where I can download one, I am happy to make a >> probe package and then we will make it available via biocLite(). >> >> Best, >> >> Jim >> >> >> >> Simens Zhong wrote: >>> Hi, all, >>> >>> >>> I got problems when normalizing HT-HG_U133A Early Access Array. What I >>> did >>> is as follows, >>> >>> library(u133aaofav2cdf) >>> library(affy) >>> library(gcrma) >>> >>> Data <- ReadAffy() >>> tmp <- gcrma(Data) >>> Adjusting for optical >>> effect.................................................... >>> .................................................................. ............Do >>> ne. >>> Computing affinities[1] "Checking to see if your internet connection >>> works..." >>> [1] "Environment u133aaofav2probe was not found in the Bioconductor >>> repository." >>> Error in get(x, envir, mode, inherits) : variable "u133aaofav2probe" was >>> not fou >>> nd >>> Execution halted >>> >>> >>> I did find the package "u133aaofav2cdf", but "u133aaofav2probe" seems to >>> me unavailable in bioconductor. has any idea? >>> >>> Thanks. >>> >>> SZ >>> >>> _______________________________________________ >>> 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 >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Affymetrix and cDNA Microarray Core >> University of Michigan Cancer Center >> 1500 E. Medical Center Drive >> 7410 CCGC >> Ann Arbor MI 48109 >> 734-647-5623 >> > -- James W. MacDonald, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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