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

[Wolfgang Huber]

Hi Suprabhath

a look at the man page of "normalize.AffyBatch.invariantset" shows that 
this function expects an "AffyBatch" object, while you are giving it an 
exprSet.

Why can't you use the function "normalize.invariantset"?


You could inspect the code of the function 
"normalize.AffyBatch.invariantset" (by simply typing its name into the 
command line) to see what it does and how you would interface
to normalize.invariantset.

  HTH
  Wolfgang


Suprabhath Reddy Gajjala a écrit 23/03/2008 18:58:
> 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
> 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 "indexProbes", for
> signature "exprSet", "character"
> 
> 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.
> 
> 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
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
Best wishes
  Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber