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

[Suprabhath Reddy Gajjala]

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