[BioC] Problem with read.marrayRaw

[Joyce Gu]

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 at 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 at 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 at 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 at 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 at stat.math.ethz.ch
>> >> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>> >>
>>
>>