[BioC] different probe level data at computer cluster

[Markus Schmidberger]

Hello,

to get the location of perfect matches from an AffyBatch I use the 
function pmindex().
If I send my AffyBatch to a slave and use the pmindex() function at the 
slave I get an other result than using the function at the master node.

Attached you can find some simple testcode and the sessionInfo plot.
You can see, that the same annotation package will be used at the master 
and at the slaves. Therefore there should be the same index structure. 
But there is a difference!

Any ideas for solutions?

Best regards
Markus

##################
library(snow)
c1<- makeCluster(1)

library(affy)
library(affydata)
data(Dilution)

indexMaster <- pmindex(Dilution)
indexSlave <- clusterCall(c1, function(x) { library(affy); pmindex(x)}, 
Dilution) # Returns a LIST!

all.equal(indexMaster, indexSlave[[1]])
[1] "Names: 40 string mismatches"                           
 [2] "Component 12586: Numeric: lengths (69, 20) differ"     
 [3] "Component 12587: Mean relative  difference: 1.345755"  
 [4] "Component 12588: Mean relative  difference: 0.5620998" 
 [5] "Component 12589: Mean relative  difference: 0.6626076" 
 [6] "Component 12590: Mean relative  difference: 0.487681"  
 [7] "Component 12591: Mean relative  difference: 0.4553995" 
 [8] "Component 12592: Mean relative  difference: 0.4263176" 
 [9] "Component 12593: Mean relative  difference: 0.5712674" 
[10] "Component 12594: Mean relative  difference: 0.9872221" 
[11] "Component 12595: Mean relative  difference: 0.6511257" 
[12] "Component 12596: Mean relative  difference: 1.118144"  
[13] "Component 12597: Mean relative  difference: 0.7570665" 
[14] "Component 12598: Mean relative  difference: 0.6555009" 
[15] "Component 12599: Mean relative  difference: 0.8429751" 
[16] "Component 12600: Mean relative  difference: 0.8220698" 
[17] "Component 12601: Mean relative  difference: 0.5806326" 
[18] "Component 12602: Mean relative  difference: 0.9459446" 
[19] "Component 12603: Mean relative  difference: 0.005017876"
[20] "Component 12604: Mean relative  difference: 0.002521591"
[21] "Component 12605: Mean relative  difference: 17.80169"  
[22] "Component 12606: Mean relative  difference: 0.6895796" 
[23] "Component 12607: Mean relative  difference: 1.435084"  
[24] "Component 12608: Mean relative  difference: 0.9511139" 
[25] "Component 12609: Mean relative  difference: 0.004859382"
[26] "Component 12610: Mean relative  difference: 0.002441555"
[27] "Component 12611: Mean relative  difference: 0.004895062"
[28] "Component 12612: Mean relative  difference: 0.02192048"
[29] "Component 12613: Mean relative  difference: 0.00498039"
[30] "Component 12614: Mean relative  difference: 0.002502659"
[31] "Component 12615: Mean relative  difference: 0.009985646"
[32] "Component 12616: Mean relative  difference: 0.004943459"
[33] "Component 12617: Mean relative  difference: 0.002484009"
[34] "Component 12618: Mean relative  difference: 0.009911417"
[35] "Component 12619: Mean relative  difference: 0.004907072"
[36] "Component 12620: Mean relative  difference: 0.002465635"
[37] "Component 12621: Mean relative  difference: 0.01475742"
[38] "Component 12622: Mean relative  difference: 0.002423802"
[39] "Component 12623: Mean relative  difference: 0.01259747"
[40] "Component 12624: Mean relative  difference: 0.01005289"
[41] "Component 12625: Numeric: lengths (20, 69) differ"

indexMaster[12586]
$`AFFX-hum_alu_at`
 [1] 250676 375731 211930 327074 352651 352650  43467 159539 159540 171051
[11] 231270 102022 263133 140413 278581 178848 178847 214557 191494 191495
[21]  38016 228673 277142 275902 114699 215783  77671  21489  21490 267349
[31] 276339 257960 305449 305450 279710  22853  22854 163552 336192 339896
[41]  35483  43466  43465 171053 171052 102024 102023 263134 278582 278583
[51] 277394 373143 214556  58516  58515 270948 249046 318231 126406  57395
[61] 247739 154374 154375 154376 144365 254115 254116 337311 337310

indexSlave[[1]][12586]
$`AFFX-HUMGAPDH/M33197_3_at`
 [1] 121056  36917 261006  35492 126329 176294 141533 368370 155742  84276
[11] 137751  66002   4753  26735  71484 102044 214559  25066 127497 114997

sessionInfo()
R version 2.6.0 (2007-10-03)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods 
[8] base    
other attached packages:
[1] hgu95av2cdf_2.0.0    affydata_1.11.3      affy_1.16.0        
[4] preprocessCore_1.0.0 affyio_1.6.1         Biobase_1.16.1     
[7] Rmpi_0.5-6           snow_0.2-9         
loaded via a namespace (and not attached):
[1] rcompgen_0.1-15


clusterEvalQ(c1, sessionInfo())
[[1]]
R version 2.6.0 (2007-10-03)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods 
[8] base    
other attached packages:
[1] hgu95av2cdf_2.0.0    affy_1.16.0          preprocessCore_1.0.0
[4] affyio_1.6.1         Biobase_1.16.1       snow_0.2-9         
[7] Rmpi_0.5-6         


stopCluster(c1)



-- 
Dipl.-Tech. Math. Markus Schmidberger

Ludwig-Maximilians-Universität München
IBE - Institut für medizinische Informationsverarbeitung,
Biometrie und Epidemiologie
Marchioninistr. 15, D-81377 Muenchen
URL: http://ibe.web.med.uni-muenchen.de 
Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
Tel: +49 (089) 7095 - 4599