[BioC] Error message from R2.2.0 on Linux

Tue Dec 6 23:49:58 CET 2005

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 at stat.Berkeley.EDU]
> Sent: Tuesday, December 06, 2005 2:53 PM
> To: Hua Weng
> Cc: bioconductor at 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 at stat.Berkeley.EDU]
>> Sent: Tuesday, December 06, 2005 1:42 PM
>> To: Hua Weng
>> Cc: bioconductor at 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
>>>
>>>
>>>
>>>
>>> 	[[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
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