[R] Different versions, different results ?

From: <charles-r-nospam_at_plessy.org>
Date: Wed 01 Jun 2005 - 13:54:08 EST


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

charles@tofu:~$ 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).

charles@tofu:~$ 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...

Best regards,

-- 
Charles Plessy, Ph.D. - Genome Science Laboratory
The Institute for Physical and Chemical Research (RIKEN)
2-1 Hirosawa, Wako, Saitama 351-0198, Japan
plessy@riken.jp --  Fax: 048-462-4686  --  Tel: 048-467-9515

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Received on Wed Jun 01 14:15:14 2005

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