error in drawing PCA plot

Question

[hassanlou110]

Hi, I can't draw PCA plot by this command. The following error massage appeared. I appreciated for any one help.

mydata <- ReadAffy()
eset <- rma(mydata)
plotPCA(eset, groups=as.numeric(pData(mydata)[,2]), groupnames=levels(pData(mydata)[,2]))

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘plotPCA’ for signature ‘"ExpressionSet"’

[Devon Ryan]

Try library("affy") first.

[hassanlou110]

I previously install and load affy packages, however I see that error!

[WouterDeCoster]

You need to load the library in every R session you start.

Please add the result of sessionInfo()

[hassanlou110]

These are the result of sessionInfo()

> library(affycoretools)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘Rcpp’
Error: package or namespace load failed for ‘affycoretools’
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] cluster_2.0.3       limma_3.26.9        affy_1.48.0        
[4] Biobase_2.30.0      BiocGenerics_0.16.1

loaded via a namespace (and not attached):
[1] zlibbioc_1.16.0       BiocInstaller_1.20.3 
[3] DBI_0.7               tools_3.2.3          
[5] affyio_1.40.0         preprocessCore_1.32.0
[7] stats4_3.2.3

[Kevin Blighe]

Don't use plotPCA(). Use base R code: A: PCA plot from read count matrix from RNA-Seq

[Devon Ryan]

Your affycoretools installation is broken. That's where the plotPCA() function that you're trying to use should be coming from. If you fix that then it'll work.

[hassanlou110]

Thank you Ryan, do you know how can I fix that? maybe I should install this package as computer administrator?!

[Devon Ryan]

I assume it's installed as your user, so try uninstalling and reinstalling (also as your user). Presumably you'll get an error message upon reinstallation that's informative.