[BioC] Error in normalize.quantiles.robust

[James W. MacDonald]

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.
>>>
>>> _______________________________________________
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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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