4
0
Entering edit mode
Joyce Gu ▴ 200
@joyce-gu-611
Last seen 8.5 years ago
Hi, I am using marray packages to analyze my cDNA data, when I load my data with read.marrayRaw() function, I got the following error messag, 1] "Reading C:/MicroArray/cDNARawData/FormattedData/cDNA196.csv" Error in "colnames<-"(*tmp*, value = fnames) : length of dimnames[2] not equal to array extent Does anyone can give a hint? Thank you
marray marray • 978 views
0
Entering edit mode
@jean-yee-hwa-yang-104
Last seen 8.5 years ago
Hi Joyce, What is the exact command you use? Usually with read.marrayRaw, you will need to specify the column names for the Red and Green channels. In addition, what kind of image analysis files are you trying to read your data from. Cheers Jean ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jean Yee Hwa Yang jean@biostat.ucsf.edu Division of Biostatistics, Tel: (415) 476-3368 University of California, Fax: (415) 476-6014 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Thu, 22 Jan 2004, Joyce Gu wrote: > Hi, > I am using marray packages to analyze my cDNA data, > when I load my data with read.marrayRaw() function, > I got the following error messag, > 1] "Reading C:/MicroArray/cDNARawData/FormattedData/cDNA196.csv" > Error in "colnames<-"(*tmp*, value = fnames) : > length of dimnames[2] not equal to array extent > > Does anyone can give a hint? > > Thank you > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
0
Entering edit mode
Joyce Gu ▴ 200
@joyce-gu-611
Last seen 8.5 years ago
Hi Jean, I did declare Res and Green channels, I am using the following command > data196.raw<-read.marrayRaw("cDNA196.csv",sep=",",path="~/...", + name.Gf="Ch1 Median",name.Gb="Ch1 B Median",name.Rf="Ch2 Median",name.Rb="Ch2 B Median") I still got the follwoing error message [1] "Reading C:/MicroArray/cDNARawData/FormattedData/cDNA196.csv" Error in "colnames<-"(*tmp*, value = fnames) : length of dimnames[2] not equal to array extent In addition: Warning messages: 1: number of items read is not a multiple of the number of columns 2: NAs introduced by coercion 3: NAs introduced by coercion 4: NAs introduced by coercion Thanks >===== Original Message From Jean Yee Hwa Yang <jean@biostat.ucsf.edu> ===== >Hi Joyce, > >What is the exact command you use? Usually with read.marrayRaw, you will >need to specify the column names for the Red and Green channels. In >addition, what kind of image analysis files are you trying to read your >data from. > >Cheers > >Jean > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Jean Yee Hwa Yang jean@biostat.ucsf.edu > Division of Biostatistics, Tel: (415) 476-3368 > University of California, Fax: (415) 476-6014 > 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >On Thu, 22 Jan 2004, Joyce Gu wrote: > >> Hi, >> I am using marray packages to analyze my cDNA data, >> when I load my data with read.marrayRaw() function, >> I got the following error messag, >> 1] "Reading C:/MicroArray/cDNARawData/FormattedData/cDNA196.csv" >> Error in "colnames<-"(*tmp*, value = fnames) : >> length of dimnames[2] not equal to array extent >> >> Does anyone can give a hint? >> >> Thank you >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >>
0
Entering edit mode
Hi Joyce, The function assumes you have a tab delimited file. If not, you need to include the argument sep=",". If it still didn't work, please send me the file "cDNA196.csv" and I will take a look. Cheers Jean ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jean Yee Hwa Yang jean@biostat.ucsf.edu Division of Biostatistics, Tel: (415) 476-3368 University of California, Fax: (415) 476-6014 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Thu, 22 Jan 2004, Joyce Gu wrote: > Hi Jean, > I did declare Res and Green channels, I am using the following command > > > data196.raw<-read.marrayRaw("cDNA196.csv",sep=",",path="~/...", > + name.Gf="Ch1 Median",name.Gb="Ch1 B Median",name.Rf="Ch2 > Median",name.Rb="Ch2 B Median") > > I still got the follwoing error message > [1] "Reading C:/MicroArray/cDNARawData/FormattedData/cDNA196.csv" > Error in "colnames<-"(*tmp*, value = fnames) : > length of dimnames[2] not equal to array extent > In addition: Warning messages: > 1: number of items read is not a multiple of the number of columns > 2: NAs introduced by coercion > 3: NAs introduced by coercion > 4: NAs introduced by coercion > > Thanks > >===== Original Message From Jean Yee Hwa Yang <jean@biostat.ucsf.edu> ===== > >Hi Joyce, > > > >What is the exact command you use? Usually with read.marrayRaw, you will > >need to specify the column names for the Red and Green channels. In > >addition, what kind of image analysis files are you trying to read your > >data from. > > > >Cheers > > > >Jean > > > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Jean Yee Hwa Yang jean@biostat.ucsf.edu > > Division of Biostatistics, Tel: (415) 476-3368 > > University of California, Fax: (415) 476-6014 > > 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > >On Thu, 22 Jan 2004, Joyce Gu wrote: > > > >> Hi, > >> I am using marray packages to analyze my cDNA data, > >> when I load my data with read.marrayRaw() function, > >> I got the following error messag, > >> 1] "Reading C:/MicroArray/cDNARawData/FormattedData/cDNA196.csv" > >> Error in "colnames<-"(*tmp*, value = fnames) : > >> length of dimnames[2] not equal to array extent > >> > >> Does anyone can give a hint? > >> > >> Thank you > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@stat.math.ethz.ch > >> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > >> > >
0
Entering edit mode
Joyce Gu ▴ 200
@joyce-gu-611
Last seen 8.5 years ago
Hi Jean, I read the same file with function read.marrayLayout and read.marrayInfo, they all work, but not with read.marrayRaw. I also check my file, there is no extra comma after the last colume, I still got the error message as following: [1] "Reading C:/Documents and Settings/jxgu/Desktop/cDNAraw/WorkingFile/cDNA196M2.txt" Error in "colnames<-"(*tmp*, value = fnames) : length of dimnames[2] not equal to array extent In addition: Warning message: number of items read is not a multiple of the number of columns Thanks >===== Original Message From Jean Yee Hwa Yang <jean@biostat.ucsf.edu> ===== >Hi Joyce, > >The function assumes you have a tab delimited file. If not, you need to >include the argument sep=",". > >If it still didn't work, please send me the file "cDNA196.csv" and I will >take a look. > >Cheers > >Jean > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Jean Yee Hwa Yang jean@biostat.ucsf.edu > Division of Biostatistics, Tel: (415) 476-3368 > University of California, Fax: (415) 476-6014 > 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >On Thu, 22 Jan 2004, Joyce Gu wrote: > >> Hi Jean, >> I did declare Res and Green channels, I am using the following command >> >> > data196.raw<-read.marrayRaw("cDNA196.csv",sep=",",path="~/...", >> + name.Gf="Ch1 Median",name.Gb="Ch1 B Median",name.Rf="Ch2 >> Median",name.Rb="Ch2 B Median") >> >> I still got the follwoing error message >> [1] "Reading C:/MicroArray/cDNARawData/FormattedData/cDNA196.csv" >> Error in "colnames<-"(*tmp*, value = fnames) : >> length of dimnames[2] not equal to array extent >> In addition: Warning messages: >> 1: number of items read is not a multiple of the number of columns >> 2: NAs introduced by coercion >> 3: NAs introduced by coercion >> 4: NAs introduced by coercion >> >> Thanks >> >===== Original Message From Jean Yee Hwa Yang <jean@biostat.ucsf.edu> ===== >> >Hi Joyce, >> > >> >What is the exact command you use? Usually with read.marrayRaw, you will >> >need to specify the column names for the Red and Green channels. In >> >addition, what kind of image analysis files are you trying to read your >> >data from. >> > >> >Cheers >> > >> >Jean >> > >> >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> > Jean Yee Hwa Yang jean@biostat.ucsf.edu >> > Division of Biostatistics, Tel: (415) 476-3368 >> > University of California, Fax: (415) 476-6014 >> > 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 >> >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> > >> >On Thu, 22 Jan 2004, Joyce Gu wrote: >> > >> >> Hi, >> >> I am using marray packages to analyze my cDNA data, >> >> when I load my data with read.marrayRaw() function, >> >> I got the following error messag, >> >> 1] "Reading C:/MicroArray/cDNARawData/FormattedData/cDNA196.csv" >> >> Error in "colnames<-"(*tmp*, value = fnames) : >> >> length of dimnames[2] not equal to array extent >> >> >> >> Does anyone can give a hint? >> >> >> >> Thank you >> >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor@stat.math.ethz.ch >> >> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >> >> >> >>
0
Entering edit mode
Ron Ophir ▴ 80
@ron-ophir-303
Last seen 8.5 years ago
Hi Joyce, >From my experience the reason for that problem is that the number of skipped rows is not equal for all files. Check which of you input files has different number of rows to skip. I think that one of the wrappers in marrayTools solve that problem. Ron Ron Ophir, Ph.D. Bioinformatician, Biological Services Weizmann Institute of Science POB 26 Rehovot 76100 Israel e-mail: Ron.Ophir@weizmann.ac.il Phone: 972-8-9342614 Fax:972-8-9344113 >>> Joyce Gu <jwgu@bcm.tmc.edu> 01/22/04 7:53 PM >>> Hi Jean, I read the same file with function read.marrayLayout and read.marrayInfo, they all work, but not with read.marrayRaw. I also check my file, there is no extra comma after the last colume, I still got the error message as following: [1] "Reading C:/Documents and Settings/jxgu/Desktop/cDNAraw/WorkingFile/cDNA196M2.txt" Error in "colnames<-"(*tmp*, value = fnames) : length of dimnames[2] not equal to array extent In addition: Warning message: number of items read is not a multiple of the number of columns Thanks >===== Original Message From Jean Yee Hwa Yang <jean@biostat.ucsf.edu> ===== >Hi Joyce, > >The function assumes you have a tab delimited file. If not, you need to >include the argument sep=",". > >If it still didn't work, please send me the file "cDNA196.csv" and I will >take a look. > >Cheers > >Jean > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Jean Yee Hwa Yang jean@biostat.ucsf.edu > Division of Biostatistics, Tel: (415) 476-3368 > University of California, Fax: (415) 476-6014 > 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >On Thu, 22 Jan 2004, Joyce Gu wrote: > >> Hi Jean, >> I did declare Res and Green channels, I am using the following command >> >> > data196.raw<-read.marrayRaw("cDNA196.csv",sep=",",path="~/...", >> + name.Gf="Ch1 Median",name.Gb="Ch1 B Median",name.Rf="Ch2 >> Median",name.Rb="Ch2 B Median") >> >> I still got the follwoing error message >> [1] "Reading C:/MicroArray/cDNARawData/FormattedData/cDNA196.csv" >> Error in "colnames<-"(*tmp*, value = fnames) : >> length of dimnames[2] not equal to array extent >> In addition: Warning messages: >> 1: number of items read is not a multiple of the number of columns >> 2: NAs introduced by coercion >> 3: NAs introduced by coercion >> 4: NAs introduced by coercion >> >> Thanks >> >===== Original Message From Jean Yee Hwa Yang <jean@biostat.ucsf.edu> ===== >> >Hi Joyce, >> > >> >What is the exact command you use? Usually with read.marrayRaw, you will >> >need to specify the column names for the Red and Green channels. In >> >addition, what kind of image analysis files are you trying to read your >> >data from. >> > >> >Cheers >> > >> >Jean >> > >> >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> > Jean Yee Hwa Yang jean@biostat.ucsf.edu >> > Division of Biostatistics, Tel: (415) 476-3368 >> > University of California, Fax: (415) 476-6014 >> > 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 >> >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> > >> >On Thu, 22 Jan 2004, Joyce Gu wrote: >> > >> >> Hi, >> >> I am using marray packages to analyze my cDNA data, >> >> when I load my data with read.marrayRaw() function, >> >> I got the following error messag, >> >> 1] "Reading C:/MicroArray/cDNARawData/FormattedData/cDNA196.csv" >> >> Error in "colnames<-"(*tmp*, value = fnames) : >> >> length of dimnames[2] not equal to array extent >> >> >> >> Does anyone can give a hint? >> >> >> >> Thank you >> >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor@stat.math.ethz.ch >> >> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >> >> >> >> _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor