Hello,
I would like to use for 42 experiments "as.numeric" (objects of type
'"numeric"')
I wrote in such a way:
> library(affy)
> data.raw <- ReadAffy(filenames= "./R/ME_cel/Expt1_R1.CEL",
... "./R/ME_cel/Expt14_R3.CEL")
> as.numeric(sampleNames(data.raw))
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Warning message:
NAs introduced by coercion
How can I find correctly numeric values of data.raw?
Thanks,
Mohammad Esad-Djou
Mohammad,
have you tried
exprs(data.raw) or
intensity(data.raw)
Also, please consider that the software is written by and the mailing
list discussions are provided by volunteers. So before posting such a
question, please consider reading the vignette of the affy package
first, and perhaps a manual of the R language.
Best wishes
Wolfgang
Mohammad Esad-Djou wrote:
> Hello,
>
> I would like to use for 42 experiments "as.numeric" (objects of type
'"numeric"')
> I wrote in such a way:
>
>
>>library(affy)
>>data.raw <- ReadAffy(filenames= "./R/ME_cel/Expt1_R1.CEL",
>
> ... "./R/ME_cel/Expt14_R3.CEL")
>
>
>>as.numeric(sampleNames(data.raw))
>
> [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA
> [26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> Warning message:
> NAs introduced by coercion
>
>
> How can I find correctly numeric values of data.raw?
>
> Thanks,
> Mohammad Esad-Djou
>
>
Best regards
Wolfgang
-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax: +44 1223 494486
Http: www.ebi.ac.uk/huber
Thank you for your answer.
> have you tried
>
> exprs(data.raw) or
> intensity(data.raw)
>
Yes, I already tried exprs(data.raw).
Unfortunately does not help me. I simplified my question, so that it
can be answered concretely.
I will read again R manual.
best Regards,
Mohammad
Wolfgang Huber <huber@ebi.ac.uk> schrieb am 30.05.05 13:18:38:
>
> Mohammad,
>
> Also, please consider that the software is written by and the
mailing
> list discussions are provided by volunteers. So before posting such
a
> question, please consider reading the vignette of the affy package
> first, and perhaps a manual of the R language.
>
> Best wishes
> Wolfgang
>
> Mohammad Esad-Djou wrote:
> > Hello,
> >
> > I would like to use for 42 experiments "as.numeric" (objects of
type '"numeric"')
> > I wrote in such a way:
> >
> >
> >>library(affy)
> >>data.raw <- ReadAffy(filenames= "./R/ME_cel/Expt1_R1.CEL",
> >
> > ... "./R/ME_cel/Expt14_R3.CEL")
> >
> >
> >>as.numeric(sampleNames(data.raw))
> >
> > [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA
> > [26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> > Warning message:
> > NAs introduced by coercion
> >
> >
> > How can I find correctly numeric values of data.raw?
> >
> > Thanks,
> > Mohammad Esad-Djou
> >
> >
>
>
> Best regards
> Wolfgang
>
> -------------------------------------
> Wolfgang Huber
> European Bioinformatics Institute
> European Molecular Biology Laboratory
> Cambridge CB10 1SD
> England
> Phone: +44 1223 494642
> Fax: +44 1223 494486
> Http: www.ebi.ac.uk/huber
> -------------------------------------
What Wolfgang is implying is that it is a rather strange thing you
want
to do. Your command was
as.numeric(sampleNames(data.raw))
with data.raw an AffyBatch object. Now,
sampleNames(data.raw)
will return you a vector of sampleNames, which is a character vector
with names associated with each sample. I believe the default is to
put
the filenames there. So the command
sampleNames(data.raw)
should return a vector of filesnames. It is not at all clear how these
filenames should be converted to numbers. Compare
> as.numeric(c("1","2","3"))
[1] 1 2 3
> as.numeric(c("a","b","c"))
[1] NA NA NA
Warning message:
NAs introduced by coercion
Kasper
On Mon, May 30, 2005 at 01:47:49PM +0200, Mohammad Esad-Djou wrote:
> Thank you for your answer.
>
> > have you tried
> >
> > exprs(data.raw) or
> > intensity(data.raw)
> >
> Yes, I already tried exprs(data.raw).
> Unfortunately does not help me. I simplified my question, so that it
can be answered concretely.
> I will read again R manual.
>
> best Regards,
> Mohammad
>
>
>
> Wolfgang Huber <huber@ebi.ac.uk> schrieb am 30.05.05 13:18:38:
> >
> > Mohammad,
> >
> > Also, please consider that the software is written by and the
mailing
> > list discussions are provided by volunteers. So before posting
such a
> > question, please consider reading the vignette of the affy package
> > first, and perhaps a manual of the R language.
> >
> > Best wishes
> > Wolfgang
> >
> > Mohammad Esad-Djou wrote:
> > > Hello,
> > >
> > > I would like to use for 42 experiments "as.numeric" (objects of
type '"numeric"')
> > > I wrote in such a way:
> > >
> > >
> > >>library(affy)
> > >>data.raw <- ReadAffy(filenames= "./R/ME_cel/Expt1_R1.CEL",
> > >
> > > ... "./R/ME_cel/Expt14_R3.CEL")
> > >
> > >
> > >>as.numeric(sampleNames(data.raw))
> > >
> > > [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA
> > > [26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> > > Warning message:
> > > NAs introduced by coercion
> > >
> > >
> > > How can I find correctly numeric values of data.raw?
> > >
> > > Thanks,
> > > Mohammad Esad-Djou
> > >
> > >
> >
> >
> > Best regards
> > Wolfgang
> >
> > -------------------------------------
> > Wolfgang Huber
> > European Bioinformatics Institute
> > European Molecular Biology Laboratory
> > Cambridge CB10 1SD
> > England
> > Phone: +44 1223 494642
> > Fax: +44 1223 494486
> > Http: www.ebi.ac.uk/huber
> > -------------------------------------
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
Kasper Daniel Hansen, Research Assistant
Department of Biostatistics, University of Copenhagen
See comments below.
On Mon, 2005-05-30 at 13:08 +0200, Mohammad Esad-Djou wrote:
> Hello,
>
> I would like to use for 42 experiments "as.numeric" (objects of type
'"numeric"')
> I wrote in such a way:
>
> > library(affy)
> > data.raw <- ReadAffy(filenames= "./R/ME_cel/Expt1_R1.CEL",
> ... "./R/ME_cel/Expt14_R3.CEL")
Can you try to use the following instead please
raw <- ReadAffy( filenames=c("Expt1_R1.CEL", "Expt14_R3.CEL"),
celfile.path="./R/ME_cel/" )
I am aware that you do not need the "c" for ReadAffy() to work but it
is
conventional with R when quote it as an array.
> > as.numeric(sampleNames(data.raw))
> [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA
> [26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> Warning message:
> NAs introduced by coercion
As the warning says and as demonstrated by Kasper, the NA's you get is
from coercion of string characters.
> How can I find correctly numeric values of data.raw?
It would have helped if you shown the output of sampleNames(data.raw)
or
what you mean by numeric values.
Assuming you want to extract the value of "14" from Expt14_R3.CEL, try
cn <- c("Expt1_R1.CEL", "Expt14_R3.CEL")
# replace this with cn <- sampleNames(data.raw)
tmp <- strsplit( cn, split="_" )
tmp <- sapply( cn, function(x) unlist(strsplit(x, split="_"))[[1]] )
gsub("Expt", "", tmp)
[1] "1" "14"
as.numeric( gsub("Expt", "", tmp) )
[1] 1 14
If I assume that you want to extract "3" from Expt14_R3.CEL, try
instead
tmp <- strsplit( cn, split="_" )
tmp <- sapply( cn, function(x) unlist(strsplit(x, split="_"))[[2]] )
as.numeric( gsub( "R", "", gsub(".CEL", "", tmp) ) )
Next time, please learn to ask the question more clearly (with example
of the desired output) to avoid the rest of guessing (e.g. what do you
mean by "correctly finding numeric values").
> Thanks,
> Mohammad Esad-Djou
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
