[BioC] Error in normalize.quantiles.robust

DAVID ARTETA GARCIA darteta001 at ikasle.ehu.es
Wed Jul 2 14:14:53 CEST 2008


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


Can anyone help me with this?

TIA,

D.



More information about the Bioconductor mailing list