Question: error in drawing MDS plot for eset
0
gravatar for Shamim Sarhadi
3.7 years ago by
Shamim Sarhadi20 wrote:

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
..
 

ADD COMMENTlink modified 3.7 years ago by James W. MacDonald52k • written 3.7 years ago by Shamim Sarhadi20

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 

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Shamim Sarhadi20
Answer: error in drawing MDS plot for eset
0
gravatar for James W. MacDonald
3.7 years ago by
United States
James W. MacDonald52k wrote:

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?

ADD COMMENTlink written 3.7 years ago by James W. MacDonald52k

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

,your code works correctly 

 

ADD REPLYlink written 3.7 years ago by Shamim Sarhadi20
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