[BioC] Error in normalize.quantiles.robust

[DAVID ARTETA GARCIA]

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
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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
>>> Phone: (206) 667-2793
>>>
>>>
>>
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