[BioC] PCA plots and identifying outliers

[Kasoji, Manjula (NIH/NCI) [C]]

Thanks! I'll look into it

On 10/5/12 12:06PM, "James W. MacDonald" <jmacdon at uw.edu> wrote:

>Please don't take things off-list! We hope that the list archives will
>be useful to others.
>
>On 10/5/2012 11:52 AM, Kasoji, Manjula (NIH/NCI) [C] wrote:
>> Thanks for the quick response, Jim. I can't believe I missed that in the
>> documentation. I can add text to the 2d plot, but I was unable to do it
>> for the 3d plot. Is this feature not available for 3d?
>
>Not using plotPCA(). I use rgl for the 3d plotting, and haven't really
>explored it enough to add the text to the plot.
>
>However, you can easily do something close to what you want.
>
>pca <- prcomp(t(exprs(eset)))
>text3d(pca$x[,1:3], text = sampleNames(eset))
>
>You will likely need to fiddle around with things to get what you like,
>but that is the general idea.
>
>Best,
>
>Jim
>
>
>
>>
>> Thanks!
>>
>>
>>
>>
>> On 10/5/12 11:41AM, "James W. MacDonald"<jmacdon at uw.edu>  wrote:
>>
>>> Hi Guest,
>>>
>>> On 10/5/2012 11:35 AM, Guest [guest] wrote:
>>>> Hi,
>>>>
>>>> I'm using affycoretools() to generate some pca plots. I found that I
>>>> have some outliers. I was wondering, how do I find out which
>>>>particular
>>>> sample (.CEL file) was the outlier?
>>>>
>>>>    I know which group it is from, but not the identity.
>>>>
>>>> I've plotted pca plots with just using the plot() function as well,
>>>>but
>>>> I still do not know how to identify the particular sample that is the
>>>> outlier.
>>>>
>>>> Any ideas for both affycoretools() or the general plot() function will
>>>> be appreciated!
>>> See ?plotPCA, in particular the addtext argument.
>>>
>>> plotPCA(eset, groups, groupnames, addtext = sampleNames(eset))
>>>
>>> Best,
>>>
>>> Jim
>>>
>>>
>>>> Thanks,
>>>>
>>>> Guest
>>>>
>>>>    -- output of sessionInfo():
>>>>
>>>> No error, just question about how find out further details.
>>>>
>>>> --
>>>> Sent via the guest posting facility at bioconductor.org.
>>>>
>>>> _______________________________________________
>>>> 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
>>> University of Washington
>>> Environmental and Occupational Health Sciences
>>> 4225 Roosevelt Way NE, # 100
>>> Seattle WA 98105-6099
>>>
>
>-- 
>James W. MacDonald, M.S.
>Biostatistician
>University of Washington
>Environmental and Occupational Health Sciences
>4225 Roosevelt Way NE, # 100
>Seattle WA 98105-6099
>