Question: normalize.AffyBatch.vsn not expressed in vsn
0
gravatar for Claudio Lottaz
3.0 years ago by
Claudio Lottaz40 wrote:

Hi all,

I use the function expresso from the affy package for normalizing microarray data, and tell expresso to use vsn as normalization method. This went fine for years but the current version of vsn (3.42.3) no longer exports the normalize.AffyBatch.vsn method. Hence, expresso no longer finds vsn as normalization method. Is this a bug or intention? If I force the export, expresso seems to execute vsn-normalisation as expected.

Cheers,

Claudio

 

affy vsn software error • 548 views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Claudio Lottaz40
Answer: normalize.AffyBatch.vsn not expressed in vsn
0
gravatar for James W. MacDonald
3.0 years ago by
United States
James W. MacDonald51k wrote:

It's still there for me.

> library(affy)

> library(vsn)
> normalize.AffyBatch.methods()
[1] "constant"         "contrasts"        "invariantset"     "loess"         
[5] "methods"          "qspline"          "quantiles"        "quantiles.robust"
[9] "vsn"           
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C            
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8  
[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8 
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C               
[9] LC_ADDRESS=C               LC_TELEPHONE=C          
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] vsn_3.42.3          affy_1.52.0         Biobase_2.34.0   
[4] BiocGenerics_0.20.0

loaded via a namespace (and not attached):
[1] Rcpp_0.12.7           lattice_0.20-34       assertthat_0.1     
[4] plyr_1.8.4            grid_3.3.1            gtable_0.2.0       
[7] scales_0.4.1          ggplot2_2.2.0         BiocInstaller_1.24.0
[10] zlibbioc_1.20.0       lazyeval_0.2.0.9000   affyio_1.44.0      
[13] limma_3.30.3          preprocessCore_1.36.0 tools_3.3.1        
[16] munsell_0.4.3         compiler_3.3.1        colorspace_1.3-0   
[19] tibble_1.2         
>
ADD COMMENTlink written 3.0 years ago by James W. MacDonald51k
Answer: normalize.AffyBatch.vsn not expressed in vsn
0
gravatar for Claudio Lottaz
3.0 years ago by
Claudio Lottaz40 wrote:

Oops, it seems that I messed up my previous installation (with vsn version 3.42.0). Now thinks work fine for me as well.Thanks for the hint!

Cheers, Claudio

ADD COMMENTlink written 3.0 years ago by Claudio Lottaz40
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