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]
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
--
Ingrid H.G. ?stensen
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
Ingrid H.G. ?stensen 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.
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. ??stensen 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. ?stensen
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