[EMAIL PROTECTED] wrote:
Dear all,
I wrote the following batch script on a iMac, and ran it on a linux
mosix cluster.
tu <- read.table("cage.mm5.tags.rna_lib.CAA-CAJ.tu-reshape.table")
tu_reshaped <- t(reshape(tu[1:50,], direction="wide", timevar="tu",
idvar=c("rna","lib")))
write.table(tu_reshaped, "cage.mm5.tags.rna_lib.CAA-CAJ.tu-reshaped.table")
q(sav="no")
(I will remove the [1:50,] later, the table has 153,646 rows)
The original tables are identical on both machines :
$ head cage.mm5.tags.rna_lib.CAA-CAJ.tu-reshape.table
"rna" "lib" "tu" "x"
"1" "CAA" "114BA" "1" 2
"2" "CAB" "114BA" "1" 5
"3" "CAC" "114BA" "1" 1
"4" "CAD" "114BA" "1" 5
"5" "CAG" "114BA" "1" 4
"6" "CAH" "114BA" "1" 2
"7" "CAI" "114BA" "1" 6
"8" "CAJ" "114BA" "1" 2
"9" "CAA" "114BB" "1" 1
The written table, however, is different :
GSLC8|Reproducibility|$ head cage.mm5.tags.rna_lib.CAA-CAJ.tu-reshaped.table
"1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" "16" "17" "18" "19" "20" "21" "22" "23" "24" "27" "35" "38" "44" "47" "50"
"rna" "CAA" "CAB" "CAC" "CAD" "CAG" "CAH" "CAI" "CAJ" "CAA" "CAB" "CAD" "CAE" "CAF" "CAG" "CAH" "CAI" "CAJ" "CAA" "CAB" "CAD" "CAG" "CAH" "CAI"
"CAJ" "CAE" "CAE" "CAE" "CAJ" "CAF" "CAD"
"lib" "114BA" "114BA" "114BA" "114BA" "114BA" "114BA" "114BA" "114BA" "114BB" "114BB" "114BB" "114BB" "114BB" "114BB" "114BB" "114BB" "114BB" "114BC" "114BC" "114BC"
"114BC" "114BC" "114BC" "114BC" "114BC" "114BA" "061AA" "061AA" "114BA" "062AA"
"x.1" " 2" " 5" " 1" " 5" " 4" " 2" " 6" " 2" " 1" " 5" " 3" " 4" " 2" " 2" " 1" " 2" " 1" " 1" " 2" " 1" "
1" " 1" " 1" " 2" NA NA NA NA NA NA
"x.2" NA " 1" NA NA NA NA NA NA NA NA " 1" NA NA NA NA NA NA NA NA NA NA NA NA NA "
1" NA NA NA NA NA
"x.4" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA " 1" NA NA NA NA
NA NA NA NA NA NA
"x.5" NA NA NA NA NA NA " 2" " 1" NA " 2" " 1" NA NA NA NA NA " 1" NA NA NA NA NA "
1" NA NA NA NA NA NA NA
"x.7" NA NA NA NA NA NA " 1" NA " 1" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
" 1" NA NA NA NA
"x.24" " 1" " 2" NA NA NA NA NA NA NA NA " 3" NA " 1" NA NA NA NA NA NA NA NA NA NA NA "
1" NA " 1" NA NA NA
"x.114" NA NA " 1" NA NA NA " 1" NA NA NA NA NA NA NA NA NA NA NA " 1" NA NA NA NA NA NA " 1" NA
" 1" " 1" NA
[EMAIL PROTECTED]:~$ head cage.mm5.tags.rna_lib.CAA-CAJ.tu-reshaped.table
"X1" "X2" "X3" "X4" "X5" "X6" "X7" "X8" "X9" "X10" "X11" "X12" "X13" "X14" "X15" "X16" "X17" "X18" "X19" "X20" "X21" "X22" "X23" "X24"
"X27" "X35" "X38" "X44" "X47" "X50"
"rna" "CAA" "CAB" "CAC" "CAD" "CAG" "CAH" "CAI" "CAJ" "CAA" "CAB" "CAD" "CAE" "CAF" "CAG" "CAH" "CAI" "CAJ" "CAA" "CAB" "CAD" "CAG" "CAH" "CAI"
"CAJ" "CAE" "CAE" "CAE" "CAJ" "CAF" "CAD"
"lib" "114BA" "114BA" "114BA" "114BA" "114BA" "114BA" "114BA" "114BA" "114BB" "114BB" "114BB" "114BB" "114BB" "114BB" "114BB" "114BB" "114BB" "114BC" "114BC" "114BC"
"114BC" "114BC" "114BC" "114BC" "114BC" "114BA" "061AA" "061AA" "114BA" "062AA"
"x.1" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5"
"2" "5" "2" "5"
"x.2" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA""x.4" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA""x.5" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA""x.7" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA"
"NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA""x.24" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA"
"x.114" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA"
"NA" "NA" "NA" "NA" "NA" "NA"
There is something obviously wrong in the second one. The versions are:
GSLC8|Reproducibility|$ R --version
R 2.1.0 Patched (2005-05-12).
[EMAIL PROTECTED]:~$ R --version
R 1.5.1 (2002-06-17).
I am wondering wether there is a fix or I have to ask the admin of the mosix
cluster to upgrade R...
Yes, yes:
Yes there is a fix: R has been fixed more than once in the last 3 year.
More precisely, there have been 12 *releases* in the meantime.
So please upgrade!
Uwe Ligges
Best regards,
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