[BioC] warning (condition has length>1) when reading in Agilent hyb text files

[Seth Falcon]

Hi John,

John Fernandes <jfernand at stanford.edu> writes:
>> However, I am getting results from the weight function.  Does the warning
>> indicate a problem?

It is difficult to say whether the warning message indicates a problem
with the results returned by the function.  

>> I am getting a warning for each file:
>>
>>     "the condition has length > 1 and only the first element will be used
>> in: if (text.to.search != "") for (i in 1:ncn)"

This means that the text.to.search variable is a vector with length
greater than 1 and that the if statement is only using the first
element for the logical test.  Whether or not this is a real problem
requires a more thorough understanding of the code.

> Anyone have an idea what could be causing the warning I'm getting?  Do  
> you need more info from me?  Can I look up the error somewhere?

If you want to get more details you could do:

   debug(read.maimages)

And then run your example and step through what read.maimages is
doing.  You will be able to inspect variables by printing them and
will likely be able to gain more information.  ANother way to identify
this is to turn warnings into errors using options() and set the error
response to recover:  

   options(warn=4, error=recover)

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org