Hello all,
I am new to bioconductor and I am running into a couple of problems
converting a marrayNorm object to an exprSet object. I convert the
marrayNorm object to an exprSet using the following:
library("convert")
xEset <- as(marrayNorm object, "exprSet")
The problem is that there does not seem to be any probe level
information in the exprSet i.e.
> geneNames(monkey)
NULL
> featureNames(monkey)
Error in featureNames(monkey) : no direct or inherited method for
function 'featureNames' for this call
This information is available in the marrayNorm object:
> norm at maGnames@maInfo[1:10,]
ID Name
X22170 22170 DXF68S1E
X21642 21642 ABCA2
X22209 22209 LOC56990
X22121 22121 PDZD2
X24284 24284 PACE
X66999 66999 CD74
X110223 110223 DLD
X110202 110202 EEF1A1
X21744 21744 GGA2
X22739 22739 FLJ14566
I can fix the gene names by doing the following
geneNames(monkey) <- norm at maGnames@maInfo$Name
but the same does not work with the feature names. Is the correct way
to do this? Anyway round the feature name problem.
Many thanks
Daniel Brewer
--
**************************************************************
Daniel Brewer, Ph.D.
Institute of Cancer Research
Hi Daniel --
Your work-around for adding geneNames to 'monkey' is the way to go --
here the problem is in the convert package, so perhaps the package
maintainer will incorporate a fix.
A featureNames method didn't exist for exprSet (it will in the next
release), so for now geneNames is the way to access the information
you want from an exprSet.
Martin
Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> writes:
> Hello all,
>
> I am new to bioconductor and I am running into a couple of problems
> converting a marrayNorm object to an exprSet object. I convert the
> marrayNorm object to an exprSet using the following:
>
> library("convert")
> xEset <- as(marrayNorm object, "exprSet")
>
> The problem is that there does not seem to be any probe level
> information in the exprSet i.e.
>> geneNames(monkey)
> NULL
>> featureNames(monkey)
> Error in featureNames(monkey) : no direct or inherited method for
> function 'featureNames' for this call
>
> This information is available in the marrayNorm object:
>> norm at maGnames@maInfo[1:10,]
> ID Name
> X22170 22170 DXF68S1E
> X21642 21642 ABCA2
> X22209 22209 LOC56990
> X22121 22121 PDZD2
> X24284 24284 PACE
> X66999 66999 CD74
> X110223 110223 DLD
> X110202 110202 EEF1A1
> X21744 21744 GGA2
> X22739 22739 FLJ14566
>
> I can fix the gene names by doing the following
>
> geneNames(monkey) <- norm at maGnames@maInfo$Name
>
> but the same does not work with the feature names. Is the correct
way
> to do this? Anyway round the feature name problem.
>
> Many thanks
>
> Daniel Brewer
>
> --
> **************************************************************
>
> Daniel Brewer, Ph.D.
>
> Institute of Cancer Research
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
Daniel Brewer wrote:
> Hello all,
>
> I am new to bioconductor and I am running into a couple of problems
> converting a marrayNorm object to an exprSet object. I convert the
> marrayNorm object to an exprSet using the following:
>
> library("convert")
> xEset <- as(marrayNorm object, "exprSet")
>
> The problem is that there does not seem to be any probe level
> information in the exprSet i.e.
>
>>geneNames(monkey)
>
> NULL
>
>>featureNames(monkey)
>
> Error in featureNames(monkey) : no direct or inherited method for
> function 'featureNames' for this call
>
> This information is available in the marrayNorm object:
>
>>norm at maGnames@maInfo[1:10,]
>
> ID Name
> X22170 22170 DXF68S1E
> X21642 21642 ABCA2
> X22209 22209 LOC56990
> X22121 22121 PDZD2
> X24284 24284 PACE
> X66999 66999 CD74
> X110223 110223 DLD
> X110202 110202 EEF1A1
> X21744 21744 GGA2
> X22739 22739 FLJ14566
>
> I can fix the gene names by doing the following
>
> geneNames(monkey) <- norm at maGnames@maInfo$Name
>
> but the same does not work with the feature names. Is the correct
way
> to do this? Anyway round the feature name problem.
Hi, Daniel. Welcome to bioconductor.
The geneNames slot of an exprSet is meant to hold the unique name for
each feature on the array, like the affy probeset id, for example. It
can hold the actual names of genes, but then will probably not be
unique. In the larger picture, the exprSet is not meant to hold any
annotation at all. It was designed to be used in conjunction with a
bioconductor annotation package. I personally find exprSets a bit
difficult to use when I am using my own annotation, just for this
reason. What array platform are you using and what are you trying to
accomplish with converting to an exprSet?
Sean
> Hi, Daniel. Welcome to bioconductor.
>
> The geneNames slot of an exprSet is meant to hold the unique name
for
> each feature on the array, like the affy probeset id, for example.
It
> can hold the actual names of genes, but then will probably not be
> unique. In the larger picture, the exprSet is not meant to hold any
> annotation at all. It was designed to be used in conjunction with a
> bioconductor annotation package. I personally find exprSets a bit
> difficult to use when I am using my own annotation, just for this
> reason. What array platform are you using and what are you trying
to
> accomplish with converting to an exprSet?
>
> Sean
I am using custom made cDNA arrays (and later on BACs etc. but always
two colour arrays). The current approach that I am using is
genepix->marray->exprSet. From there I am interested in doing quite a
bit of analysis including differential analysis, clustering etc. and
then when I have interesting lists go down the annotation path. I
would
like the cloneIDs (unique identifyer) to be always associated with the
current working object, which does not seem to be the case at the
moment.
I was under the impression that the way that bioconductor worked, was
to
use one of a number of approaches to get to the an exprSet object and
then use that object to do all the analysis. Please correct me if I
am
mistaken.
Thanks again
Daniel