[BioC] agi4x44preprocess

[Michael Dondrup]

Hi,
looks like you just got a '.' too much in the header line in your
targets file: 'File.Name' vs 'FileName'.

Best

Am 28.10.2009 um 20:17 schrieb Neel Aluru:

> Hi Tobias,
>
> Thanks for your help. I tried your suggestion and it keeps giving me  
> a new error message. Here are the details of my trials.
>
> > library("Agi4x44PreProcess")
> Loading required package: Biobase
> Welcome to Bioconductor
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
> Loading required package: limma
> Loading required package: annotate
> Loading required package: AnnotationDbi
> Loading required package: genefilter
>
> > getwd()
> [1] "/Users/Neel/agilent"
> > targets=read.targets(infile="infile.txt")
>
> Target File
>      X File.Name Treatment GErep
> 1 cont1 conta.txt   control     1
> 2 cont2 contb.txt   control     2
> 3 cont3 contc.txt   control     3
> 4 cont4 contd.txt   control     4
> 5  pcb1  pcba.txt       pcb     1
> 6  pcb2  pcbb.txt       pcb     2
> 7  pcb3  pcbc.txt       pcb     3
> 8  pcb4  pcbd.txt       pcb     4
>
> > read.AgilentFE(targets, makePLOT)
> Error in read.maimages(files = targets$FileName, source = "agilent",  
> other.columns = list(IsFound = "gIsFound",  :
>  Must specify input files
>
> It is able to recognize the infile which has all the details of the  
> files. Also, all the files are in the same directory. Cannot  
> understand why it cannot recognize the files.
>
> Any help will be greatly appreciated.
>
> Sincerely, Neel
>
> On Oct 27, 2009, at 11:59 AM, Tobias Straub wrote:
>
>> what about
>> >targets = read.targets(infile="infile.txt")
>> >read.AgilentFE(targets, makePLOT)
>>
>> best
>> T.
>>
>> On Oct 27, 2009, at 4:43 PM, Neel Aluru wrote:
>>
>>> Hello,
>>>
>>> I am just beginning to work with Bioconductor and started having  
>>> issues, which I think are minor but cannot figure out myself. I  
>>> started using Agi4x44preprocess and the first step went fine. That  
>>> is
>>>
>>> >targets = read.targets(infile="infile.txt")
>>> This loads my list of files and treatments as a data.frame.
>>> My problem is with the next step.
>>> >read.AgilentFE(infile, makePLOT)
>>>
>>> I get an error message, "Error in is(targets, "data.frame") :  
>>> object 'infile' not found". I have the infile and all the  
>>> agilentFE text files in my working directory. Not sure where I am  
>>> doing it wrong.
>>>
>>> Any help is appreciated.
>>>
>>> Sincerely, Neel
>>>
>>> Neel Aluru
>>> Postdoctoral Scholar
>>> Biology Department
>>> Woods Hole Oceanographic Institution
>>> Woods Hole, MA 02543
>>> USA
>>>
>>> _______________________________________________
>>> 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
>>
>> ----------------------------------------------------------------------
>> Dr. Tobias Straub ++4989218075439 Adolf-Butenandt-Institute,  
>> München D
>>
>>
>>
>>
>>
>>
>
> Neel Aluru
> Postdoctoral Scholar
> Biology Department
> Woods Hole Oceanographic Institution
> Woods Hole, MA 02543
> USA
> 508-289-3607
>
> _______________________________________________
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> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
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Michael Dondrup, Ph.D.
Bergen Center for Computational Science
Computational Biology Unit
Unifob AS - Thormøhlensgate 55, N-5008 Bergen, Norway
Phone: +47 55584029 Fax: +47 55584295