[BioC] Differences between Linux and Windows

[Wolfgang Huber]

Dear Ingrid,

This could be (among other things)
(1) a floating-point round-off error together with the thresholds you
use, or
(2) a consequence of some randomization / subsampling in one the
algorithms you use; for example, gcrma does that.

To diagnose this, you could
(2) Use "set.seed(12345)" at the start of the script and see if you then
get more identical results
(1) wiggle your p-value cutoff (or whatever you do, you didn't say that)
a bit

 Best wishes
 Wolfgang



Ingrid H. G. Østensen wrote:
> Hi
> 
> I have run the same script on Linux and on Windows (sessionInfo are below) and I get different number of differentially expressed genes out in my VennDiagram. When I use Windows I get 53929 genes that do not belong anywhere, 667 in one group, 11 in the other and 68 that they have in common. When I run this on Linux I get 53930 genes that do not belong anywhere, 663 in one group, 14 in the other and 68 that they have in common. There is not much difference but it is a difference, any idea why? Both R/Bioconductors have been updated within the last 14 days or so.
> 
> 
>> sessionInfo()
> R version 2.4.1 (2006-12-18)
> i686-pc-linux-gnu
> 
> locale:
> C
> 
> attached base packages:
> [1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
> [7] "datasets"  "methods"   "base"
> 
> other attached packages:
> hgu133plus2probe   hgu133plus2cdf      hgu133plus2          annaffy
>         "1.14.0"         "1.14.0"         "1.14.0"          "1.6.1"
>             KEGG               GO         annotate            gcrma
>         "1.14.1"         "1.14.1"         "1.12.1"          "2.6.0"
>      matchprobes           xtable     RColorBrewer     affyQCReport
>          "1.6.0"          "1.4-3"          "0.2-3"         "1.12.0"
>       simpleaffy       genefilter         survival             affy
>          "2.8.0"         "1.12.0"           "2.30"         "1.12.2"
>           affyio          Biobase            limma
>          "1.2.0"         "1.12.2"          "2.9.8"
> 
> 
> 
>> sessionInfo()
> R version 2.4.1 (2006-12-18) 
> i386-pc-mingw32 
> 
> locale:
> LC_COLLATE=Norwegian (Bokmål)_Norway.1252;LC_CTYPE=Norwegian (Bokmål)_Norway.1252;LC_MONETARY=Norwegian (Bokmål)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokmål)_Norway.1252
> 
> attached base packages:
> [1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"   "base"     
> 
> other attached packages:
> hgu133plus2probe   hgu133plus2cdf      hgu133plus2          annaffy             KEGG               GO 
>         "1.14.0"         "1.14.0"         "1.14.0"          "1.6.1"         "1.14.1"         "1.14.1" 
>         annotate            gcrma      matchprobes           xtable     RColorBrewer     affyQCReport 
>         "1.12.1"          "2.6.0"          "1.6.0"          "1.4-3"          "0.2-3"         "1.12.0" 
>       simpleaffy       genefilter         survival             affy           affyio          Biobase 
>          "2.8.0"         "1.12.0"           "2.30"         "1.12.2"          "1.2.0"         "1.12.2" 
>            limma 
>          "2.9.8" 
> 
> Regards,
> Ingrid
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber