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

Francois Pepin francois at sus.mcgill.ca
Fri Apr 23 21:47:49 CEST 2010


Hi Julia,

sorry for taking a while for replying, I was away on a conference. Also, replying to the list means that other people can also offer advice and that the conversation will be archived in case other people have this issue.

That seems like that the file should be of the proper format from the scanner and the file name.

Do all of your files fail, or is there only a specific one that has this issue?

Francois

On Apr 16, 2010, at 7:19 AM, Turner, Julia wrote:

> Hi Francois,
> 
> 1. The scanner is a G2505B.  
> 2. Here is an example file name: E2F1_251486828858_S01_GE1_107_Sep09_1_3.txt
> 3. I was just using setwd("\\\") as an example I am not really setting my working directory to that location:). 
> 
> Thanks,
> Julia
> 
> -----Original Message-----
> From: Francois Pepin [mailto:francois at sus.mcgill.ca] 
> Sent: Thursday, April 15, 2010 12:52 PM
> To: Turner, Julia
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Agi4x44PreProcess_1.6.0 Error in readGenericHeader(fullname, columns = columns, sep = sep) :
> 
> 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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> 
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