[BioC] Error message from R2.2.0 on Linux
Hua Weng
hweng at biochem.okstate.edu
Tue Dec 6 21:16:04 CET 2005
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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