[BioC] agi4x44preprocess

[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
>>
>> _______________________________________________
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>
> ----------------------------------------------------------------------
> 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