Dear list,
I am dealing with between group analysis (BGA) from the made4 package
and I have a problem with some of the affy names:
I tried
bga.suppl(training.set[list,], supdata=test.set[list,],
classvec=cl_train, supvec=cl_test)
'training.set' and 'test.set' are expression sets, and 'cl_train' and
'cl_test' the corresponding classification vectors.
'list' contains some selected affy IDs.
>list
[1] "217367_s_at" "202880_s_at" "1565905_at" "236347_at" ...
I tried bga with different lists, and in most cases, this works fine.
But however, sometimes the following error message appears:
Error in "dimnames<-.data.frame"(`*tmp*`, value =
list(c("217367_s_at", :
invalid 'dimnames' given for data frame
It has definitively to do with the selected identifiers, and I have
the
impression that made4 can not manage identifiers with an minus sign
inside, such as:
AFFX-HUMGAPDH/M33197_M_at
AFFX-BioDn-3_at
I am running
ade4 (Version: 1.4-2) and made4 (Version: 1.8.0) under R 2.3.1
Has somebody an idea how to handle this problem?
Thanks in advance,
Heike
--
Dr. Heike Pospisil | pospisil at zbh.uni-hamburg.de
University of Hamburg | Center for Bioinformatics
Bundesstrasse 43 | 20146 Hamburg, Germany
phone:+49-40-42838-7303 | fax: +49-40-42838-7312
Dear Heike
I have not encountered this problem with Affy data, but it sounds like
a
R error caused by moving between a matrix and data.frame. I convert
affy data using data.frame(exprs(arraydata)), as ade4 expects data in
data.frame.
Can you email me a subset of the data which is giving you this
problem.
Or can you run a traceback() on this, so I can pin-point the
problem.
Thanks a million
Aedin
>I tried bga with different lists, and in most cases, this works
fine.
>But however, sometimes the following error message appears:
>Error in "dimnames<-.data.frame"(`*tmp*`, value =
list(c("217367_s_at",
>
> invalid 'dimnames' given for data frame
>
--
Aed?n Culhane,
Research Associate in Prof. J Quackenbush Lab
Harvard School of Public Health, Dana-Farber Cancer Institute
44 Binney Street, SM822 ****Please note change of address****
Department of Biostatistics and Computational Biology,
Dana-Farber Cancer Institute
Boston, MA 02115
USA
Phone: +1 (617) 632 2468
Fax: +1 (617) 582 7760
Email: aedin at jimmy.harvard.edu
Web URL: http://www.hsph.harvard.edu/researchers/aculhane.html
Dear Heike,
This was a bug in made4. I have corrected this in the devel version
of
made4. I attach this bug-fix in the enclosed R code. Please source
this
file and bga should run without problems.
As an aside, if read.table will automatically create a data.frame, so
you don't need to do as.data.frame.
data<-as.data.frame(read.table(file=paste(dir,"data2.txt",sep=""),head
er=TRUE,row.names="ID"))
> data1 <-read.table("data2.txt",header=TRUE,row.names="ID")
> class(data1)
[1] "data.frame"
made4 will read in ExpressionSet, matrix, data.frame or most
bioconductor data classes. So you don't need to convert to a
data.frame
before running bga.
Although possible, its generally not advised to call an object the
same
name as a function.
list<-rownames(data)[1:26]
I am very sorry about the bug. Thanks a million for brining it to my
attention.
Kinds Regards
Aedin
Heike Pospisil wrote:
> Dear Aedin,
>
> thank you for your fast reply.
>
>> I have not encountered this problem with Affy data, but it sounds
like
>> a R error caused by moving between a matrix and data.frame.
>
>
> Yes, this could be. But I did not find the error :-(
>
>> I convert affy data using data.frame(exprs(arraydata)), as ade4
>> expects data in data.frame.
>
>
> So did I.
>
>> Can you email me a subset of the data which is giving you this
>> problem. Or can you run a traceback() on this, so I can pin-point
the
>> problem.
>
>
> I prepared a fictitious expression set and attached it in two
versions:
> - example.Rdata is the ExpressionSet
> - data2.txt contains the expressions as a matrix
>
> You can load either the Rdata or the txt file:
> #############################################
> ##### Load Data ######
> #############################################
> dir<-your.download.directory
> data<-as.data.frame(read.table(file=paste(dir,"data2.txt",sep=""),he
ader=TRUE,row.names="ID"))
>
> ######## or ###############
> load(paste(dir,"example.Rdata",sep=""))
> data1<-exprs(data2)
> data<-as.data.frame(data1)
>
>
> #############################################
> ##### BGA #####
> #############################################
> cl_training<-c(0,0,1,1)
> cl_testing<-c(0,0,1,1)
>
> list<-rownames(data)[1:26]
> bga.suppl(data[list,1:4],
supdata=data[list,5:8],classvec=cl_training,
> supvec=cl_testing)
>
> It works very fine with the first 26 probe sets. But it crashes if I
> select the first 27 probes:
>
> list<-rownames(data)[1:27]
> bga.suppl(data[list,1:4],
supdata=data[list,5:8],classvec=cl_training,
> supvec=cl_testing)
>
> Error in "dimnames<-.data.frame"(`*tmp*`, value = list(c("65884_at",
> "66053_at", :
> invalid 'dimnames' given for data frame
>
> Hope, it is clear what I meant and I hope you can load my dummy
data.
>
> Would be great if you could help me.
>
> Thanks a lot and best wishes,
> Heike
>
>
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