Ok Hua, I have been pointed to the solution.

You original post has something like

<SNIP>

>>> "Wavelengths=650	546"	

<SNIP>

>>> Block	Column	Row	Name	ID	X	Y	Dia.	F650 Median
>>> F650 Mean	F650 SD	B650 Median	B650 Mean	B650 SD	% > B650 1SD
>>> % > B650 2SD	F650 % Sat.	F546 Median	F546 Mean	F546 SD	B546
>>> Median	B546 Mean	B546 SD	% > B546 1SD	% > B546 2SD	F546

Notice the wavelengths and the column headers (B650, F645)

You try to read this using

>>>>> RG <- read.maimages(files, columns=list(R="F532 Mean", G="F635
>>>>> Mean", Rb="B532 Median", Gb="B635 Median"), wt.fun=wtflags(0.1))

That actually works on the file you sent me, because that file has

"Wavelengths=635	532"

<SNIP>

"Block"	"Column"	"Row"	"Name"	"ID"	"X"	"Y"	"Dia."	"F635 Median"	"F635  
Mean"	"F635 SD"	"B635 Median"	"B635 Mean"	"B635 SD"	"% > B635 1SD"	"%  
 > B635 2SD"	"F635 % Sat."	"F532 Median"	"F532 Mean"	"F532 SD"	"B532  
Median"	"B532 Mean"	"B532 SD"	"% > B532 1SD"	"% > B532 2SD"	"F532 %  
Sat."	"Ratio of Medians (532/635)"	"Ratio of Means (532/635)"	"Median  
of Ratios (532/635)"	"Mean of Ratios (532/635)"	"Ratios SD  
(532/635)"	"Rgn Ratio (532/635)"	"Rgn R² (532/635)"	"F Pixels"	"B  
Pixels"	"Sum of Medians"	"Sum of Means"	"Log Ratio (532/635)"	"F635  
Median - B635"	"F532 Median - B532"	"F635 Mean - B635"	"F532 Mean -  
B532"	"F635 Total Intensity"	"F532 Total Intensity"	"SNR 635"	"SNR  
532"	"Flags"	"Normalize"

In this file the wavelengths and the column headers (B635, F532) are  
different from before (B650, F645).

My guess is that you (or however did the scanning) have scanned the  
arrays with different wavelengths. At least you have different column  
headers in the different files.

I am not an expert on scanning technology, but my guess is that this  
will be really hard to fix. If you want to try anyway (in the hope  
that normalization will take care of the wavelength issue), you need  
to read the files into two different objects in limma and then  
subsequently merge them.

Since this is a user error, the only reason I can imagine for the  
code to run on windows and not on linux is that you have two  
(different) set of files....

/Kasper


On Dec 6, 2005, at 2:49 PM, Kasper Daniel Hansen wrote:

> It parses fine on the linux system I have access to (which is a bit
> different, it is 64 bit, uses limma 2.4.2 and does not run the
> standard release version of R).
>
> I think I may be wrong about the locale stuff. But you can do a bit
> of debuging
>
> 1) check the files argument: is it really the list of files you want
> (no "wrong" files?)
> 2) you migth want to specify the sources argument to the
> read.maimages function
> 3) check that
>    R> for(fileName in files) readLines(fileName, n = 100)
> actually runs (this checks thar R can read the header of each file in
> the files vector you defined in your first email.
> 4) try to debug the function to see what is wrong, ie. try
>    R> debug(read.maimages)
> now you can step through the function one line at a time. Try to
> figure out what file/ line it bangs out on.
>
> Beyond that I am not sure I can be of much help as I am unable to
> reproduce the problem and I am fairly unfamiliar with read.maimages.
>
> But try step 1-4.
>
> Kasper
>
> On Dec 6, 2005, at 1:29 PM, Hua Weng wrote:
>
>> Dear Kasper:
>>
>> I attaches the file header fro you to review. I highly appreciate
>> your help.
>>
>> Hua
>>
>> -----Original Message-----
>> From: Kasper Daniel Hansen [mailto:khansen@stat.Berkeley.EDU]
>> Sent: Tuesday, December 06, 2005 2:53 PM
>> To: Hua Weng
>> Cc: bioconductor@stat.math.ethz.ch
>> Subject: Re: [BioC] Error message from R2.2.0 on Linux
>>
>> Unfortunately, the mail system has scrambled the specifics of your
>> message. Try doing something like this (on Linux):
>>
>> # head -100 FILENAME > file.header
>> # gzip file.header
>>
>> and then mail me the header.
>>
>> A big change recently have been how R handles character sets, so I am
>> not surprised that this is an issue. I am not sure I can help you in
>> details (you might want to try R-help), but I can help you isolate
>> the problem. Your LANG seems standard.
>>
>> Kasper
>>
>>
>> On Dec 6, 2005, at 12:16 PM, Hua Weng wrote:
>>
>>>
>>>
>>> Dear Kasper:
>>>
>>> Thank you very much for your response.
>>>
>>> When I took a look at #env, my LANG=en_US.UTF-8
>>>
>>> Actually, I can read these files on the same machine in R1.8.0
>>> environment.
>>> But in R2.2.0, I got the following locale error.
>>>
>>> The following is the header part of my gpr file:
>>>
>>> ATF	1
>>> 27	82
>>> Type=GenePix Results 2	
>>> DateTime=2005/10/01 20:10:53	
>>> Settings=D:\USERS\DeSilva\asitha\GAL Files\good
>>> gals_3Plates_3X2reps\Hyb4_brahma_6hours_01oct05.gps	
>>> GalFile=D:\USERS\DeSilva\asitha\GAL Files\good
>>> gals_3Plates_3X2reps
>>> \3_plates_2x3_reps_4x4_pins_printed083005_Modnew7.gal
>>>
>>> PixelSize=10	
>>> "Wavelengths=650	546"	
>>> "ImageFiles=D:\USERS\DeSilva\asitha\TIME POINT HYBS\BRAHMA\FIBRO Vs
>>> 6HRS\TIF
>>> SCAN1\Alexa 647_P60_L78_Brahma_Hyb4_6Hrs_13300853_01oct05.tif 0
>>> D:\USERS\DeSilva\asitha\TIME POINT HYBS\BRAHMA\FIBRO Vs 6HRS\TIF
>>> SCAN1\Alexa
>>> 546_P66_L79_Brahma_Hyb4_Fibro_13300853_01Oct05.tif 0"	
>>> NormalizationMethod=None	
>>> "NormalizationFactors=1	1"	
>>> JpegImage=D:\USERS\DeSilva\asitha\TIME POINT HYBS\BRAHMA\FIBRO Vs
>>> 6HRS\non
>>> normalized results\Brahma_Hyb4_6Hrs_13300853_10Nov05_0001.jpg	
>>> RatioFormulations=W1/W2 (650/546)	
>>> Barcode=	
>>> BackgroundSubtraction=LocalFeature	
>>> "ImageOrigin=0, 0"	
>>> "JpegOrigin=1610, 4830"
>>>
>>> Creator=GenePix Pro 4.0.1.17						
>>> "Scanner=Express	430529	EXP430529"				
>>> FocusPosition=0
>>>
>>> Temperature=0								
>>> LinesAveraged=1
>>>
>>> comment=
>>>
>>> "PMTGain=0	0"
>>>
>>> "ScanPower=100	100"
>>>
>>> "LaserPower=0	0"
>>>
>>> "LaserOnTime=0	0"
>>>
>>> "ScanRegion=0,0,2200,7300"
>>>
>>> Supplier=
>>>
>>> Block	Column	Row	Name	ID	X	Y	Dia.	F650 Median
>>> F650 Mean	F650 SD	B650 Median	B650 Mean	B650 SD	% > B650 1SD
>>> % > B650 2SD	F650 % Sat.	F546 Median	F546 Mean	F546 SD	B546
>>> Median	B546 Mean	B546 SD	% > B546 1SD	% > B546 2SD	F546
>> % Sat.
>>> F3 Median	F3 Mean	F3 SD	B3 Median	B3 Mean	B3 SD	% > B3 1SD
>>> % > B3 2SD	F3 % Sat.	F4 Median	F4 Mean	F4 SD	B4 Median
>>> B4 Mean	B4 SD	% > B4 1SD	% > B4 2SD	F4 % Sat.
>> Ratio of
>>> Medians (650/546)	Ratio of Means (650/546)	Median of Ratios
>>> (650/546)	Mean of Ratios (650/546)	Ratios SD (650/546)	Rgn
>>> Ratio (650/546)	Rgn R² (650/546)	Ratio of Medians (Ratio/2)
>>> Ratio of Means (Ratio/2)	Median of Ratios (Ratio/2)	Mean of
>>> Ratios (Ratio/2)	Ratios SD (Ratio/2)	Rgn Ratio (Ratio/2)	Rgn
>>> R² (Ratio/2)	Ratio of Medians (Ratio/3)	Ratio of Means (Ratio/3)
>>> Median of Ratios (Ratio/3)	Mean of Ratios (Ratio/3)	Ratios SD
>>> (Ratio/3)	Rgn Ratio (Ratio/3)	Rgn R² (Ratio/3)	F Pixels
>>> B Pixels	Sum of Medians	Sum of Means	Log Ratio (650/546)	Log
>>> Ratio (Ratio/2)	Log Ratio (Ratio/3)	F650 Median - B650	F546
>> Median
>>> - B546	F3 Median - B3	F4 Median - B4	F650 Mean - B650	F546
>> Mean -
>>> B546	F3 Mean - B3	F4 Mean - B4	Flags	Normalize
>>>
>>> Thank you very much for your time.
>>>
>>> Hua
>>> -----Original Message-----
>>> From: Kasper Daniel Hansen [mailto:khansen@stat.Berkeley.EDU]
>>> Sent: Tuesday, December 06, 2005 1:42 PM
>>> To: Hua Weng
>>> Cc: bioconductor@stat.math.ethz.ch
>>> Subject: Re: [BioC] Error message from R2.2.0 on Linux
>>>
>>>
>>> On Dec 6, 2005, at 10:04 AM, Hua Weng wrote:
>>>
>>>> Hi, All:
>>>>
>>>> Is there anybody have problem running limma 2.2.4 from R 2.2.0 on
>>>> Linux? I can run the same code for Limma 2.2.4 from R2.2.0 on
>>>> windows without any problem. The following is information for R
>>>> and limma on linux:
>>>>
>>>>> version
>>>>          _
>>>> platform i686-pc-linux-gnu
>>>> arch     i686
>>>> os       linux-gnu
>>>> system   i686, linux-gnu
>>>> status
>>>> major    2
>>>> minor    2.0
>>>> year     2005
>>>> month    10
>>>> day      06
>>>> svn rev  35749
>>>> language R
>>>>
>>>> limma        "limma"        "/usr/local/R/lib/R/library" "2.4.4"
>>>>
>>>> And the following is the error message from the command:
>>>>> library(limma)
>>>>> files <- dir(pattern=".gpr")
>>>>> RG <- read.maimages(files, columns=list(R="F532 Mean", G="F635
>>>>> Mean", Rb="B532 Median", Gb="B635 Median"), wt.fun=wtflags(0.1))
>>>> Error in switch(source2, quantarray = { : Cannot find column
>>>> heading in image output file
>>>> In addition: Warning message:
>>>> input string 32 is invalid in this locale in: grep(pattern, x,
>>>> ignore.case, extended, value, fixed, useBytes)
>>>>
>>>> I highly appreciate any comments and suggestions for this error.
>>>
>>> Guess: you are reading in a textfile which contains non-standard
>>> characters, eg. special letters etc. You are currently operating  
>>> in a
>>> local which does not support this particular character, so either
>>> change the locale or change the file. I see you are based in the US,
>>> so I am a bit surprised that you are having problems with this.
>>>
>>> Do a
>>> # env
>>> from the shell to get a list of variables, I think the locale one is
>>> called
>>>   LANG
>>> (if you have variables such as LC_**** they override the LANG
>>> settings).
>>>
>>> However, I would change the file. Further debugging requires a look
>>> at the header of the file.
>>>
>>> Kasper
>>>
>>>> Hua Weng
>>>> Microarray Core Facility
>>>> 348E Noble Research Center
>>>> Department of Biochemistry and Molecular Biology
>>>> Oklahoma State University
>>>> Stillwater,  OK  74078
>>>> Phone:  405-744-6199
>>>> Fax:  405-744-7799
>>>>
>>>>
>>>>
>>>>
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>>>>
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>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>
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