[BioC] Agi4x44PreProcess_1.6.0 Error in readGenericHeader(fullname, columns = columns, sep = sep) :

[Francois Pepin]

Hi Julia,

we're going to need a bit more information before we can help you, although we do appreciate the sessionInfo and code snippet.

Which scanner are you using? Could you give us a few examples of the file names that you are getting from it?

My guess is that you're not using the same file format as what is expected, although a more obscure bug is also possible.

Out of curiosity, why are you setting your working directory to '///'? First it should only get you to the root directory (so '/' is enough) and second, it seems like a strange place to put your files.

Cheers,

Francois

On Apr 13, 2010, at 11:04 AM, Turner, Julia wrote:

> Hi,
> 
> I am getting the error ,
> 
> Error in readGenericHeader(fullname, columns = columns, sep = sep) :
>  Specified column headings not found in file
> 
> This happens when I try to used the read.AgilentFE function.    I have noticed other posts about the limma package, but I believe this is not the same.  My session info is:
> 
> R version 2.10.1 (2009-12-14)
> i386-pc-mingw32
> 
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                           LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] mgug4122a.db_2.3.6      org.Mm.eg.db_2.3.6      RSQLite_0.8-4           DBI_0.2-5               Agi4x44PreProcess_1.6.0
> [6] genefilter_1.28.2       annotate_1.24.1         AnnotationDbi_1.8.2     limma_3.2.3             Biobase_2.6.1
> 
> loaded via a namespace (and not attached):
> [1] splines_2.10.1  survival_2.35-7 tools_2.10.1    xtable_1.5-6
> 
> Commands:
>> library(Agi4x44PreProcess)
>> library(mgug4122a.db)
>> setwd("///")
>> targets =  read.targets(infile="target_test.txt")
>> dd=read.AgilentFE(targets, makePLOT=FALSE)
> 
> Thank you for your time and I apologize if this is posted elsewhere.  If it has already been addressed could you please forward me the thread.
> Best,
> Julia
> 
> 
> 
> 
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