[BioC] Error message from R2.2.0 on Linux

Tue Dec 6 21:53:11 CET 2005

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]]
>>
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>