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This is an R script for array quality metrics. The first step is going well but after the execution of the 2nd step an error occurs.

library(arrayQualityMetrics)

library(limma)

library(tcltk)
X <-tk_choose.files(caption = "Choose X")

maData<-read.maimages(X, source="agilent", other.columns = "g", green.only=TRUE)

eSet<-new("ExpressionSet", exprs = maData$other$g, annotation =maData$genes[,7])

arrayQualityMetrics(eSet, outdir="QC_C", force = TRUE, do.logtransform = TRUE)

The program is running now but it is showing this warning message:

The directory 'QC_C' has been created.
Warning messages:

1: In svgStyleAttributes(style) :
  Removing non-SVG style attribute name(s): subscripts, group.number, group.value

2: In svgStyleAttributes(style) :
  Removing non-SVG style attribute name(s): subscripts, group.number, group.value

Where am I getting wrong? Is this the errors in the file or the Rscript is wrong....

llrs
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Aaryan
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1 Answers1

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Give the full path of the folder under path as below:

scanFiles<-dir(path='/path/to/folder/',pattern = ".*.txt$")
Joswin K J
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  • Thanks @user3169080. I will check and get back to you – Aaryan Jun 16 '15 at 13:22
  • Your 3rd line, ie, `eSet<-new..` , is also being executed with the second line. That is the cause of the error. The end part of the error message `..green.only=TRUE)eSet` gives that. – Joswin K J Jun 17 '15 at 06:28
  • I have edited the Rscript above in the question. Have a look on it and suggest some thing ..........@user3169080 – Aaryan Jun 17 '15 at 07:12
  • Are you getting the output correctly? Warnings can be ignored in that case. – Joswin K J Jun 17 '15 at 08:11
  • I am getting the output with warnings, but I want to intergrate this Rscript into Java GUI. As when i am calling this script in the java GUI code it is not running at all , not giving any answers , just terminating to else condition for "could not complete". So, I am thinking may be it is because of the warnings that is causing problem.......@user3169080 – Aaryan Jun 17 '15 at 08:23
  • Use `options(warn=-1)`. Refer [link](http://stackoverflow.com/questions/16194212/how-to-suppress-warnings-globally-in-an-r-script) – Joswin K J Jun 17 '15 at 08:27
  • by using options(warn=-1) warnings are not comming but still I am not able to use this whole arrayQualityMetrics Rscript in the Java code. Basically I want to call this code in java, now it is running from command prompt but when I am mounting it in the java code it is not showing any errors but, shifting to the next else part that "it could not be completed" I don't know what is the problem....any suggestions – Aaryan Jun 17 '15 at 08:51