[BioC] Problem with read.marrayRaw

[Ron Ophir]

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 at weizmann.ac.il
Phone: 972-8-9342614
Fax:972-8-9344113
>>> Joyce Gu <jwgu at 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 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
>> >>
>>
>>

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