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.name s=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

On Sun, Mar 23, 2008 at 2:58 PM, Suprabhath Reddy Gajjala <sgajjala at="" emich.edu=""> 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()". Ilumina data are actually quite different in many respects from Affy data. You will be better off looking at the beadarray or lumi packages. In particular, in the beadarray package, you would use readBeadSummaryData() followed by rankInvariantNormalise() to accomplish the task you stated in your email. Rank invariant normalization has some drawbacks, the largest one, in my opinion, being the generation of negative values. Both the lumi and beadarray packages have multiple other normalization methods available. Sean

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 ?crit 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.na mes=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(0.0 03, > 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