[BioC] Error in normalize.quantiles.robust

[DAVID ARTETA GARCIA]

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.
>>
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>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M2 B169
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>
>