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 -- View this message in context: http://www.nabble.com/Error-in-function-%28classes%2C-fdef%2C-mtable%29%3A-unable-to-find-an-inherited-method-for-function-%22indexProbes%22%2C-for-signature-%22exprSet%22%2C-%22character%22-tp16190637p16190637.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.