[BioC] Error in normalize.quantiles.robust

[Martin Morgan]

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.
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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