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

From: Martin Morgan <mtmorgan_at_fhcrc.org>
Date: Thu, 20 Mar 2008 16:49:24 -0700

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More comments below...

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

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793

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