[BioC] Error message from R2.2.0 on Linux
Hua Weng
hweng at biochem.okstate.edu
Tue Dec 6 22:29:00 CET 2005
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
>
More information about the Bioconductor
mailing list