Hi, On Wed, Jul 2, 2008 at 8:36 AM, DAVID ARTETA GARCIA <darteta001 at="" ikasle.ehu.es=""> wrote: > Hi James, > > row.names is an argument indeed but it doesn?t seem to be the problem > either; I still get the same error: > >> xxx <- read.table("mydata.txt", sep = "\t", header=TRUE,row.names=1, >> colClasses="numeric") > > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, > : > scan() expected 'a real', got 'A0001' > > I have found out that for normalize.quantiles.robust() this works fine: > > aaa <- matrix(rnorm(100),ncol=5) > colnames(aaa) <-c("aa","bb","cc","dd","ee") > zzz <- normalize.quantiles.robust(aaa) > > but this does not: > > aaa <- matrix(c(15:114),ncol=5) dim <- dim(aaa); aaa <- as.double(aaa); dim(aaa) <- dim; Should solve it. /Henrik > colnames(aaa) <-c("aa","bb","cc","dd","ee") > zzz <- normalize.quantiles.robust(aaa) > Error in normalize.quantiles.robust(aaa) : > REAL() can only be applied to a 'numeric', not a 'integer' > > > This is my session info: > >> sessionInfo() > > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] affy_1.18.0 preprocessCore_1.2.0 affyio_1.8.0 > Biobase_2.0.0 > > > D. > > "James W. MacDonald" <jmacdon at="" med.umich.edu=""> ha escrito: > >> Hi David, >> >> I think you also need a row.names = 1 in your call to read.table. Check >> ?read.table to make sure - I don't have R on this computer so I can't >> check myself. >> >> Best, >> >> Jim >> >> >> >> DAVID ARTETA GARCIA wrote: >>> >>> Dear Martin, thanks for your answer. I cannot make your first suggestion >>> work: >>> >>>> xxx <- read.table("mydata.txt", sep = "\t", >>>> header=TRUE,colClasses="numeric") >>> >>> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, >>> na.strings, : >>> scan() expected 'a real', got 'A0001' >>> >>> I also tried removing the row.names and then I get >>> >>>> log.quant.rob.norm <-normalize.quantiles.robust(as.numeric(xxx)) >>> >>> Error in normalize.quantiles.robust(as.numeric(xxx)) : >>> INTEGER() can only be applied to a 'integer', not a 'NULL' >>> >>> >>> Any more thoughts? >>> >>> D. >>> >>> >>> >>> Martin Morgan <mtmorgan at="" fhcrc.org=""> ha escrito: >>> >>>> Hi David -- >>>> >>>> DAVID ARTETA GARCIA <darteta001 at="" ikasle.ehu.es=""> writes: >>>> >>>>> Dear list, I have a matrix I imported using read.table with raw >>>>> intensity data for 12 samples and 2300 genes in one colour, as folows: >>>>> >>>>>> dim(xxx) >>>>> >>>>> [1] 2352 12 >>>>> >>>>>> head(xxx) >>>>> >>>>> 0025 0039 0041 0043 0047 0058 0061 0067 0072 0073 0078 0085 >>>>> A0001 953 509 1669 867 6672 1526 453 397 883 686 382 429 >>>>> A0002 1769 641 1635 1357 4364 1308 552 441 888 1374 493 693 >>>>> A0003 2304 943 2701 1745 4966 1622 807 591 1283 1579 517 870 >>>>> A0004 2185 1235 3992 1866 6462 1556 1004 781 1512 1911 762 906 >>>>> A0005 1842 1008 1904 1434 6331 1155 759 515 1155 1448 510 764 >>>>> A0006 1586 909 2294 641 7729 1367 788 489 1317 714 503 301 >>>>> >>>>> >>>>>> class(xxx) >>>>> >>>>> [1] "matrix" >>>>> >>>>> >>>>> I am trying to normalize using robust quantiles but I get an error >>>>> that I don?t understand. >>>>> >>>>>> log.quant.rob.norm<-normalize.quantiles.robust(xxx,use.log2=TRUE) >>>>> >>>>> Error in normalize.quantiles.robust(xxx, use.log2 = TRUE) : >>>>> REAL() can only be applied to a 'numeric', not a 'integer' >>>>>> >>>>>> is.numeric(xxx) >>>>> >>>>> [1] TRUE >>>> >>>> I guess is.integer(xxx) returns TRUE; integer is a subclass of >>>> numeric, so they are both TRUE. You'll want to convert your intensity >>>> measures to numeric (e.g., with the colClasses="numeric" argument to >>>> whatever read.* function you used, or as.numeric(xxx). >>>> >>>> Martin >>>> >>>>> >>>>> Can anyone help me with this? >>>>> >>>>> TIA, >>>>> >>>>> D. >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> -- >>>> 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 >>>> >>>> >>> >>> _______________________________________________ >>> 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 > > _______________________________________________ > 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 >

Hi David, Note that the colClasses argument really wants a vector, and includes the column names as well (see ?read.table). So you want something like colClasses = rep(c("character", "numeric"), c(1, 5)) Where the c(1,5) needs to be adjusted for the number of numeric columns in your original table. Best, Jim DAVID ARTETA GARCIA wrote: > Hi James, > > row.names is an argument indeed but it doesn?t seem to be the problem > either; I still get the same error: > >> xxx <- read.table("mydata.txt", sep = "\t", header=TRUE,row.names=1, >> colClasses="numeric") > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, > na.strings, : > scan() expected 'a real', got 'A0001' > > I have found out that for normalize.quantiles.robust() this works fine: > > aaa <- matrix(rnorm(100),ncol=5) > colnames(aaa) <-c("aa","bb","cc","dd","ee") > zzz <- normalize.quantiles.robust(aaa) > > but this does not: > > aaa <- matrix(c(15:114),ncol=5) > colnames(aaa) <-c("aa","bb","cc","dd","ee") > zzz <- normalize.quantiles.robust(aaa) > Error in normalize.quantiles.robust(aaa) : > REAL() can only be applied to a 'numeric', not a 'integer' > > > This is my session info: > >> sessionInfo() > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > > attached base packages: > [1] tools stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] affy_1.18.0 preprocessCore_1.2.0 affyio_1.8.0 > Biobase_2.0.0 > > > D. > > "James W. MacDonald" <jmacdon at="" med.umich.edu=""> ha escrito: > >> Hi David, >> >> I think you also need a row.names = 1 in your call to read.table. Check >> ?read.table to make sure - I don't have R on this computer so I can't >> check myself. >> >> Best, >> >> Jim >> >> >> >> DAVID ARTETA GARCIA wrote: >>> Dear Martin, thanks for your answer. I cannot make your first >>> suggestion work: >>> >>>> xxx <- read.table("mydata.txt", sep = "\t", >>>> header=TRUE,colClasses="numeric") >>> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, >>> na.strings, : >>> scan() expected 'a real', got 'A0001' >>> >>> I also tried removing the row.names and then I get >>> >>>> log.quant.rob.norm <-normalize.quantiles.robust(as.numeric(xxx)) >>> Error in normalize.quantiles.robust(as.numeric(xxx)) : >>> INTEGER() can only be applied to a 'integer', not a 'NULL' >>> >>> >>> Any more thoughts? >>> >>> D. >>> >>> >>> >>> Martin Morgan <mtmorgan at="" fhcrc.org=""> ha escrito: >>> >>>> Hi David -- >>>> >>>> DAVID ARTETA GARCIA <darteta001 at="" ikasle.ehu.es=""> writes: >>>> >>>>> Dear list, I have a matrix I imported using read.table with raw >>>>> intensity data for 12 samples and 2300 genes in one colour, as >>>>> folows: >>>>> >>>>>> dim(xxx) >>>>> [1] 2352 12 >>>>> >>>>>> head(xxx) >>>>> 0025 0039 0041 0043 0047 0058 0061 0067 0072 0073 0078 0085 >>>>> A0001 953 509 1669 867 6672 1526 453 397 883 686 382 429 >>>>> A0002 1769 641 1635 1357 4364 1308 552 441 888 1374 493 693 >>>>> A0003 2304 943 2701 1745 4966 1622 807 591 1283 1579 517 870 >>>>> A0004 2185 1235 3992 1866 6462 1556 1004 781 1512 1911 762 906 >>>>> A0005 1842 1008 1904 1434 6331 1155 759 515 1155 1448 510 764 >>>>> A0006 1586 909 2294 641 7729 1367 788 489 1317 714 503 301 >>>>> >>>>> >>>>>> class(xxx) >>>>> [1] "matrix" >>>>> >>>>> >>>>> I am trying to normalize using robust quantiles but I get an error >>>>> that I don?t understand. >>>>> >>>>>> log.quant.rob.norm<-normalize.quantiles.robust(xxx,use.log2=TRUE) >>>>> Error in normalize.quantiles.robust(xxx, use.log2 = TRUE) : >>>>> REAL() can only be applied to a 'numeric', not a 'integer' >>>>>> is.numeric(xxx) >>>>> [1] TRUE >>>> >>>> I guess is.integer(xxx) returns TRUE; integer is a subclass of >>>> numeric, so they are both TRUE. You'll want to convert your intensity >>>> measures to numeric (e.g., with the colClasses="numeric" argument to >>>> whatever read.* function you used, or as.numeric(xxx). >>>> >>>> Martin >>>> >>>>> >>>>> Can anyone help me with this? >>>>> >>>>> TIA, >>>>> >>>>> D. >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> -- >>>> 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 >>>> >>>> >>> >>> _______________________________________________ >>> 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 > > > >

Thanks Ben and rest setting the storage mode to "double" solved the problem. I didn?t know there was a difference between a "12.73" and a "12". All the values in my data.frame were non-decimals. Guess is my lack of programming knowledge. I will look into that. Best, David DAVID ARTETA GARCIA <darteta001 at="" ikasle.ehu.es=""> ha escrito: > Hi James, > > row.names is an argument indeed but it doesn?t seem to be the > problem either; I still get the same error: > >> xxx <- read.table("mydata.txt", sep = "\t", >> header=TRUE,row.names=1, colClasses="numeric") > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : > scan() expected 'a real', got 'A0001' > > I have found out that for normalize.quantiles.robust() this works fine: > > aaa <- matrix(rnorm(100),ncol=5) > colnames(aaa) <-c("aa","bb","cc","dd","ee") > zzz <- normalize.quantiles.robust(aaa) > > but this does not: > > aaa <- matrix(c(15:114),ncol=5) > colnames(aaa) <-c("aa","bb","cc","dd","ee") > zzz <- normalize.quantiles.robust(aaa) > Error in normalize.quantiles.robust(aaa) : > REAL() can only be applied to a 'numeric', not a 'integer' > > > This is my session info: > >> sessionInfo() > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > > attached base packages: > [1] tools stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] affy_1.18.0 preprocessCore_1.2.0 affyio_1.8.0 > Biobase_2.0.0 > > > D. > > "James W. MacDonald" <jmacdon at="" med.umich.edu=""> ha escrito: > >> Hi David, >> >> I think you also need a row.names = 1 in your call to read.table. Check >> ?read.table to make sure - I don't have R on this computer so I can't >> check myself. >> >> Best, >> >> Jim >> >> >> >> DAVID ARTETA GARCIA wrote: >>> Dear Martin, thanks for your answer. I cannot make your first >>> suggestion work: >>> >>>> xxx <- read.table("mydata.txt", sep = "\t", >>>> header=TRUE,colClasses="numeric") >>> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, >>> na.strings, : >>> scan() expected 'a real', got 'A0001' >>> >>> I also tried removing the row.names and then I get >>> >>>> log.quant.rob.norm <-normalize.quantiles.robust(as.numeric(xxx)) >>> Error in normalize.quantiles.robust(as.numeric(xxx)) : >>> INTEGER() can only be applied to a 'integer', not a 'NULL' >>> >>> >>> Any more thoughts? >>> >>> D. >>> >>> >>> >>> Martin Morgan <mtmorgan at="" fhcrc.org=""> ha escrito: >>> >>>> Hi David -- >>>> >>>> DAVID ARTETA GARCIA <darteta001 at="" ikasle.ehu.es=""> writes: >>>> >>>>> Dear list, I have a matrix I imported using read.table with raw >>>>> intensity data for 12 samples and 2300 genes in one colour, as folows: >>>>> >>>>>> dim(xxx) >>>>> [1] 2352 12 >>>>> >>>>>> head(xxx) >>>>> 0025 0039 0041 0043 0047 0058 0061 0067 0072 0073 0078 0085 >>>>> A0001 953 509 1669 867 6672 1526 453 397 883 686 382 429 >>>>> A0002 1769 641 1635 1357 4364 1308 552 441 888 1374 493 693 >>>>> A0003 2304 943 2701 1745 4966 1622 807 591 1283 1579 517 870 >>>>> A0004 2185 1235 3992 1866 6462 1556 1004 781 1512 1911 762 906 >>>>> A0005 1842 1008 1904 1434 6331 1155 759 515 1155 1448 510 764 >>>>> A0006 1586 909 2294 641 7729 1367 788 489 1317 714 503 301 >>>>> >>>>> >>>>>> class(xxx) >>>>> [1] "matrix" >>>>> >>>>> >>>>> I am trying to normalize using robust quantiles but I get an error >>>>> that I don?t understand. >>>>> >>>>>> log.quant.rob.norm<-normalize.quantiles.robust(xxx,use.log2=TRUE) >>>>> Error in normalize.quantiles.robust(xxx, use.log2 = TRUE) : >>>>> REAL() can only be applied to a 'numeric', not a 'integer' >>>>>> is.numeric(xxx) >>>>> [1] TRUE >>>> >>>> I guess is.integer(xxx) returns TRUE; integer is a subclass of >>>> numeric, so they are both TRUE. You'll want to convert your intensity >>>> measures to numeric (e.g., with the colClasses="numeric" argument to >>>> whatever read.* function you used, or as.numeric(xxx). >>>> >>>> Martin >>>> >>>>> >>>>> Can anyone help me with this? >>>>> >>>>> TIA, >>>>> >>>>> D. >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> -- >>>> 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 >>>> >>>> >>> >>> _______________________________________________ >>> 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 > > _______________________________________________ > 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