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Suprabhath

2008-Mar-20 22:57 UTC

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

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
> 
> eSetExpression 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"


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 
http://www.nabble.com/file/p16190637/textE_to_affy.csv textE_to_affy.csv 
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Martin Morgan

2008-Mar-20 23:49 UTC

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

This is a Bioconductor package, ask on the Bioc mailing list

http://bioconductor.org

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

Suprabhath

2008-Mar-23 19:01 UTC

head link

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

Thankyou Martin Morgan, i will post this question in Bioconductor mailing
list <bioconductor at stat.math.ethz.ch>

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 
> 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"
> 
> 
> 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 
>  http://www.nabble.com/file/p16190637/textE_to_affy.csv textE_to_affy.csv 
> 
-- 
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