[BioC] knn.imput and prcomp error

[Ingrid H.G. Østensen]

Hi,

aneData is numeric but aneData_imp is not. But I have been told that
because of the changes in knn.impute I now have to use aneData_imput$data
instead of aneData_imp. I have tried this and now I do not get an error
message any more.

Regards,
Ingrid

> Ingrid H.G. Østensen wrote:
>> Hi
>>
>> I am running a microarray analysis that I have run before (on the same
>> data set) but now I get an error message because my matrix suddenly is
>> no
>> longer numeric. Does anybody know what happens and how do solve it?
>> Below
>> I have pasted the commands and error message.
>>
>> Ingrid
>>
>> memory.limit(1300)
>> library(limma)
>> library(impute)
>> aneTab <-
>> read.table(file="S100A4_anes.txt",sep="\t",header=T,na.strings="")
>> colnames(aneTab)
>> aneData <- aneTab[,3:14]
>
> Are all the values in andData numeric? What do you get from str(aneData)?
>
> If the values are not all numeric, when you coerce to a matrix
> everything will be coerced to some common type (often character). For
> instance, if there are factors and numeric values in your data.frame,
> they will all get coerced to character, which may be what is happening.
>
> HTH,
>
> Jim
>
>
>> aneData <- as.matrix(aneData)
>> is.matrix(aneData)
>> aneData_imp <- impute.knn(aneData)
>> aneDI_prc <-prcomp(t(aneData_imp))
>> Error in colMeans(x, n, prod(dn), na.rm) :
>>         'x' must be numeric
>>
>>
>>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not
> be used for urgent or sensitive issues.
>


-- 
Ingrid H.G. Østensen
Bioinformatics user support (NMC)
Department of Tumour Biology
The Norwegian Radiumhospital
0310 Oslo

E -mail: ingrid at microarray.no
Phone:  +47 22 93 54 11
Fax:  +47 22 52 24 21