Question

error in drawing MDS plot for eset

0

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Shamim Sarhadi ▴ 20

@shamim-sarhadi-9395

Last seen 4 months ago

Germany

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 • 1.7k views

ADD COMMENT • link updated 8.8 years ago by James W. MacDonald 67k • written 8.8 years ago by Shamim Sarhadi ▴ 20

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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

ADD REPLY • link 8.8 years ago Shamim Sarhadi ▴ 20

score 0 · Answer 1 · 2016-03-24

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Entering edit mode

James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 2 days 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?

ADD COMMENT • link 8.8 years ago James W. MacDonald 67k

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

,your code works correctly

ADD REPLY • link 8.8 years ago Shamim Sarhadi ▴ 20