error in drawing MDS plot for eset
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@shamim-sarhadi-9395
Last seen 4.7 years ago

Hi

First, I'm sorry about this minor question

I want to plot a MDSplot with plotMDS function in insilicomerging packages, I used to do this without any error or warning message, but this time I got this warning 

this is my code

plotMDS(eset1, colLabel="Disease", symLabel="Study")

 

warnings()

Warning messages:
1: "colLabel" is not a graphical parameter
2: "symLabel" is not a graphical parameter
3: "colLabel" is not a graphical parameter
4: "symLabel" is not a graphical parameter
5: "colLabel" is not a graphical parameter
6: "symLabel" is not a graphical parameter
..
 

MDSplot geneexpression insilicomerging • 831 views
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sessionInfo()

R version 3.2.4 (2016-03-10)
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  methods  
[8] base     

other attached packages:
[1] limma_3.26.8           inSilicoMerging_1.14.0 inSilicoDb_2.6.0      
[4] RCurl_1.95-4.8         bitops_1.0-6           Biobase_2.30.0        
[7] BiocGenerics_0.16.1    rjson_0.2.15           BiocInstaller_1.20.1  

loaded via a namespace (and not attached):
 [1] IRanges_2.4.8         lattice_0.20-33       Biostrings_2.38.4    
 [4] grid_3.2.4            affy_1.48.0           stats4_3.2.4         
 [7] zlibbioc_1.16.0       XVector_0.10.0        affyio_1.40.0        
[10] S4Vectors_0.8.11      latticeExtra_0.6-28   preprocessCore_1.32.0
[13] splines_3.2.4         RColorBrewer_1.1-2    gcrma_2.42.0         
[16] tools_3.2.4           affyPLM_1.46.0 

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@james-w-macdonald-5106
Last seen 5 hours ago
United States

To provide your sessionInfo, you need to include the parentheses, or else you will just get the function body (which is what you have provided here).

But do note that plotMDS is a common function name, and it is quite likely that you have loaded another package with a plotMDS defined in it that is now masking the version from insilicomerging. Does doing

insilicomerging::plotMDS(eset1, colLabel="Disease", symLabel="Study")

get things to work correctly?

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Entering edit mode

Thank you   James W. MacDonald ,I apologize for my mistake about sessionInfo()

,your code works correctly 

 

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