[R] Error in function (classes, fdef, mtable): unable to find an inherited method for function "indexProbes", for signature "exprSet", "character"

[Martin Morgan]

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Suprabhath wrote:
> Hello Everyone,
> 
> I am writing programs in R from 7 months and I am able to solve most of the
> errors/issues except for this current post. 
> 
> My Task is to read a Microsoft Excel file(textE_to_affy.csv) which contains
> the Microarray Expression Values collected from the Illumina Microarray
> experiment. These collected intensity values need to be normalized(Rank
> Invariant Normalization) by using the R function
> "normalize.AffyBatch.invariantset()". 
> 
> Since the normalize.AffyBatch.invariantset() method requires the input
> argument to be an AffyBatch Object, I used the read.exprSet() method to
> convert the intensity values present in the (textE_to_affy.csv) file into an
> AffyBatch Object as follows: 
> 
>> testFile <- tempfile()
>> textAffy<-read.table("textE_to_affy.csv",header=TRUE,sep=",",row.names=1)
>> textAffy
>                   Sample1       Sample2       Sample3
> GI_10047089-S   -6.100   -5.12500   -5.61250
> GI_10047091-S   10.725    9.70625   10.21562
> GI_10047093-S 1392.100 1378.70000 1385.40000
> GI_10047099-S  264.925  260.98125  262.95312
> GI_10047103-S 5315.675 5412.01875 5363.84688
> GI_10047105-S   21.750   22.53750   22.14375
>> write.table(TA,testFile,quote = FALSE, sep = "\t", row.names = TRUE,
>> col.names = TRUE)
>> testFile
> [1] "C:\\DOCUME~1\\Jaswanth\\LOCALS~1\\Temp\\RtmpXrUE8T\\file2ea6bb3"
>> eSet <- read.exprSet(testFile)
> Warning messages:
> 1: read.exprSet is deprecated, use readExpresionSet instead 

Pay attention to these messages. Use readExpressionSet instead!

> 2: read.phenoData is deprecated, use read.AnnotatedDataFrame instead 
> 3: The phenoData class is deprecated, use AnnotatedDataFrame (with
> ExpressionSet) instead 
> 4: The exprSet class is deprecated, use ExpressionSet instead 
> 5: The exprSet class is deprecated, use ExpressionSet instead 
> 6: The exprSet class is deprecated, use ExpressionSet instead 
> 7: The exprSet class is deprecated, use ExpressionSet instead 
> 8: The exprSet class is deprecated, use ExpressionSet instead 
> 9: The exprSet class is deprecated, use ExpressionSet instead 
>> eSet
> Expression Set (exprSet) with 
>         6 genes
>         3 samples
>         phenoData object with 1 variables and 3 cases
>         varLabels
>                 sample: arbitrary numbering
> Warning messages:
> 1: The exprSet class is deprecated, use ExpressionSet instead 
> 2: The exprSet class is deprecated, use ExpressionSet instead 
> 3: The phenoData class is deprecated, use AnnotatedDataFrame (with
> ExpressionSet) instead 
> 
>> RInormalizedData<-normalize.AffyBatch.invariantset(eSet,prd.td=c(0.003,
>> 0.007),baseline.type="mean",type="together")
> 
> Error in function (classes, fdef, mtable)  : 
>   unable to find an inherited method for function "pmindex", for signature
> "exprSet"

This error should not occur with an ExpressionSet.

> 
> I have observed that this same error message has been posted and answered in
> a different context in this forum. Even though I am not using the S4 class
> and method concepts here, I am getting this error. 

You are using a package that uses S4.

> I have also uploaded the input file on which the normalization needed to be
> performed.
> 
> Hence, I would be grateful for you if you can give some direction/advice for
> me to overcome this error. 
> 
> Thanks a lot,
> Suprabhath Reddy 
> http://www.nabble.com/file/p16190637/textE_to_affy.csv textE_to_affy.csv 


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Martin Morgan
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