[R] Different versions, different results ?

Wed Jun 1 05:54:08 CEST 2005

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 at 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 at 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 at riken.jp --  Fax: 048-462-4686  --  Tel: 048-467-9515