[BioC] pca plot for gene expression

[Michael Love]

hi Deepak,

We like to always keep the discussion on the list, to avoid having to
answer duplicate questions.

Collapsing all the patients into a single point defeats the purpose of
PCA: to see the distances between individual samples and groups of
samples. Showing just the mean for each group might mislead someone
looking at the plot into thinking the clusters are distinct, when the
samples might have high variance around that average point. I would
recommend instead just coloring the types of carcinoma.

Mike

On Wed, Jul 16, 2014 at 5:43 AM, deepak karthik <deepaksrna at gmail.com> wrote:
> Thanks for your reply.
> I have data of hundreds of patients from each carcinoma , consisting of
> rnaseq expression with certain gene of interest. If i perform pca analysis
> for numerous carcinoma  , my pca plot would be clumsy difficult to find out
> the type of carcinoma are clustered together . so i would like to mark
> single point for a particular type of carcinoma with consideration of   my
> rnaseq expression  for my  gene of my interest . Thanks in advance .
>
> with regards,
> S.Deepak
>
>
> On Tue, Jul 15, 2014 at 9:31 PM, Michael Love <michaelisaiahlove at gmail.com>
> wrote:
>>
>> You might get more feedback if you describe what kind of experiment
>> you have performed (microarray or RNA-Seq?).
>>
>> The other reason you might not be getting response is that the
>> principal component functions are not implemented in Bioconductor, but
>> in base R. So it's not necessarily a Bioconductor question, but a
>> statistics/R question.
>>
>> The very basic code for making a PCA plot from an expression set 'e' would
>> be
>>
>> pc = prcomp( t ( exprs( e ) ) )
>> plot( pc$x[ , 1:2 ] )
>>
>> On Tue, Jul 15, 2014 at 8:36 AM, karthik [guest] <guest at bioconductor.org>
>> wrote:
>> > Hi all,
>> >
>> >         I am writing this mail for second time. I wanted perform a pca
>> > analysis ,for each  cancer type and genes of interest expression. I just
>> > wanted to plot only a single  point which is able represent each cancer and
>> > their genes expression .Can you please explain me on it.( And cancer per
>> > gene basis should i take median or mean values to represent their
>> > expression). Thanks in advance.
>> >
>> >
>> >  -- output of sessionInfo():
>> >
>> > pca()
>> >
>> > --
>> > Sent via the guest posting facility at bioconductor.org.
>> >
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>
>
>
>
> --
>
> Deepak karthik
>
> PhD student
>
> +972-054-5683140
>
>
> Dr. Mali Salmon-Divon, Genomic Bioinformatics laboratory
>
> The Department of Molecular Biology
>
> Ariel University, Israel