[BioC] different probe level data at computer cluster

Richard Pearson richard.pearson at postgrad.manchester.ac.uk
Mon May 19 13:08:27 CEST 2008


Hi Markus

I just tried this myself but didn't see the problems you did. Not sure exactly why you're seeing what you do, but I note that you have Rmpi_0.5-6, whereas I believe the current release version is Rmpi_0.5-5. I'd suggest installing R 2.7.0 and using biocLite to install packages, then try again. Below is the output I got with your script - hope this helps!

Best wishes

Richard


> library(snow)
> c1<- makeCluster(1)
Loading required package: Rmpi
	1 slaves are spawned successfully. 0 failed.
> 
> library(affy)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: affyio
Loading required package: preprocessCore
> 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] TRUE
> 
> indexMaster[12586] 
$`AFFX-HUMGAPDH/M33197_3_at`
 [1] 121056  36917 261006  35492 126329 176294 141533 368370 155742  84276 137751  66002   4753  26735  71484 102044 214559  25066 127497 114997

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

> 
> sessionInfo() 
R version 2.7.0 (2008-04-22) 
i386-apple-darwin8.10.1 

locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] tools     stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] hgu95av2cdf_2.2.0    affydata_1.11.3      affy_1.18.0          preprocessCore_1.1.9 affyio_1.7.17        Biobase_2.0.0        Rmpi_0.5-5          
[8] snow_0.2-9          
> 
> clusterEvalQ(c1, sessionInfo())
[[1]]
R version 2.7.0 (2008-04-22) 
i386-apple-darwin8.10.1 

locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] hgu95av2cdf_2.2.0    affy_1.18.0          preprocessCore_1.1.9 affyio_1.7.17        Biobase_2.0.0        snow_0.2-9           Rmpi_0.5-5          


Markus Schmidberger wrote:
> 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)
> 
> 
> 

-- 
Richard D. Pearson             richard.pearson at postgrad.manchester.ac.uk
School of Computer Science,    http://www.cs.man.ac.uk/~pearsonr
University of Manchester,      Tel: +44 161 275 6178
Oxford Road,                   Mob: +44 7971 221181
Manchester M13 9PL, UK.        Fax: +44 161 275 6204



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