[BioC] Empty featureData in ExpressionSet generated by affy::justRMA
James W. MacDonald
jmacdon at med.umich.edu
Thu May 19 15:55:51 CEST 2011
Hi David,
On 5/18/2011 2:04 PM, David Shih wrote:
> Hi Jim,
>
> Thank you for clarifying the purpose of the featureData slot.
> The assayData slot also appears empty in my ExpressionSet.
It's not empty, you just didn't access it correctly.
> showMethods(exprs, class="ExpressionSet", includeDefs = TRUE)
Function: exprs (package Biobase)
object="ExpressionSet"
function (object)
assayDataElement(object, "exprs")
and
> assayDataElement
function (object, elt)
assayData(object)[[elt]]
<environment: namespace:Biobase>
So exprs() is extracting data from your assayData slot, but you have to
choose the "exprs" element of the AssayData object that assayData() returns.
>
> The rownames are missing in my expression matrix extracted using.
>> exprs(eset)
Well, they *should* be there, so this indicates some bug in the
processing. What does exprs(eset)[1:5,1:5} look like, exactly?
Best,
Jim
>
> I was hoping to fill the rownames of my matrix using keys obtained
> from
>> keys<- mappedkeys(hgu133a2ACCUM)
>
> I checked that all the keys are mapped, and I am under the impression
> that they should be for hgu133a2ACCUM.
>
> My main concern is that hgu133a2ACCUM may not return the keys
> (probe ids) in the same order as they appear in the expression matrix,
> which would cause the probes to be incorrectly mapped.
>
> I have no problem with normalizing older platforms like U133. All the
> probe ids are automatically assigned upon extraction with exprs().
> However, the hthgu133a platform does not appear to be as
> straightforward.
>
> I had a similar problems with the HT Human Gene 1.0 ST platform.
> I ended up using the oligo package, whicih provides a getNetAffx()
> function to retrieve probe annotation data.
> However, the existing normalization code precludes from switching to
> the oligo package.
>
> Best regards,
> David
>
> On Wed, May 18, 2011 at 01:51:01PM -0400, James W. MacDonald wrote:
>> Hi David,
>>
>> On 5/18/2011 1:31 PM, David Shih wrote:
>>> Dear list,
>>>
>>> I am using the affy package to normalize expression data on the HT
>>> Human Genome U133A platform. According to earlier posting on the list,
>>> this is equivalent to U133Av2.
>>>
>>> I used the justRMA() function to normalize the data, and obtained an
>>> ExpressionSet object with an empty featureData slot.
>>
>> You may be misunderstanding the purpose of the featureData slot.
>> According to ?eSet-class:
>>
>> 'featureData': Contains variables describing features (i.e., rows
>> in 'assayData') unique to this experiment. Use the
>> 'annotation' slot to efficiently reference feature data
>> common to the annotation package used in the experiment.
>> Class: 'AnnotatedDataFrame-class'
>>
>> The probeset IDs are not unique to any particular experiment, so are
>> stored as part of the assayData, which can be extracted using e.g.,
>> exprs():
>>
>>> data(sample.ExpressionSet)
>>> head(exprs(sample.ExpressionSet))
>> A B C D E
>> F G
>> AFFX-MurIL2_at 192.7420 85.75330 176.7570 135.5750 64.49390
>> 76.3569 160.5050
>> AFFX-MurIL10_at 97.1370 126.19600 77.9216 93.3713 24.39860
>> 85.5088 98.9086
>> AFFX-MurIL4_at 45.8192 8.83135 33.0632 28.7072 5.94492
>> 28.2925 30.9694
>> AFFX-MurFAS_at 22.5445 3.60093 14.6883 12.3397 36.86630
>> 11.2568 23.0034
>> AFFX-BioB-5_at 96.7875 30.43800 46.1271 70.9319 56.17440
>> 42.6756 86.5156
>> AFFX-BioB-M_at 89.0730 25.84610 57.2033 69.9766 49.58220
>> 26.1262 75.0083
>>
>> Best,
>>
>> Jim
>>
>>
>>>
>>> I understand that I can retrive the annotation information from:
>>> library(hgu133a2.db)
>>>
>>> However, I am uncertain whether the probes in the annotation library
>>> are in the same order as the ExpressionSet object.
>>>
>>> Can I add the probe IDs using the following code?
>>>
>>> library(hgu133a2.db)
>>> keys<- mappedkeys(hgu133ai2ACCNUM);
>>> expr<- exprs(eset);
>>> rownames(expr)<- keys;
>>>
>>>
>>> Best regards,
>>>
>>> David Shih, Graduate Student
>>> The Hospital for Sick Children
>>> Brain Tumour Research Centre
>>> 101 College Street, TMDT-11-401M
>>> Toronto, ON M5G1L7
>>> Canada
>>> Tel: 416-813-7654 x4327
>>>
>>>
>>>> sessionInfo()
>>> R version 2.12.2 (2011-02-25)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> locale:
>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> other attached packages:
>>> [1] hgu133a2.db_2.4.5 org.Hs.eg.db_2.4.6 RSQLite_0.9-4
>>> [4] DBI_0.2-5 AnnotationDbi_1.12.0 hthgu133acdf_2.7.0
>>> [7] affy_1.28.0 Biobase_2.10.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.2
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> Douglas Lab
>> University of Michigan
>> Department of Human Genetics
>> 5912 Buhl
>> 1241 E. Catherine St.
>> Ann Arbor MI 48109-5618
>> 734-615-7826
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and should
>> not be used for urgent or sensitive issues
>>
--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
More information about the Bioconductor
mailing list