[BioC] Data set for comparing statistical tests

[Jorge Miró]

Hi again,

I have been trying to understand how I should go on with the spike in
data but in vain.
Here are the commands I used:


************ Code *************************
> library(SpikeIn)
> data(SpikeIn133)

#Checked phenoData as suggested....
> phenoData(SpikeIn133)
An object of class "AnnotatedDataFrame"
  sampleNames: 12_13_02_U133A_Mer_Latin_Square_Expt1_R1
12_13_02_U133A_Mer_Latin_Square_Expt2_R1 ...
12_13_02_U133A_Mer_Latin_Square_Expt14_R3 (42 total)
  varLabels: 203508_at 204563_at ... AFFX-ThrX-3_at (42 total)
  varMetadata: labelDescription

# ... but I could not see the concentrations for the samples. Is it
something else I should do? I tryid with pData too and I could not
find any information about the samples concentration.

*************************** End of code ******************'
I guess the SpikeIn133 is a file with raw intensities so I shoud apply
rma on it and then use eg limma to test for differential expression of
the genes. Am I right?

I read the manual for SpikeIn but I can't see anything about  the
concentrations for each sample in the data set
(http://www.bioconductor.org/packages/2.10/data/experiment/manuals/SpikeIn/man/SpikeIn.pdf)


Best regards
Jorge

On Fri, Aug 31, 2012 at 12:01 PM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> check the SpikeIn package... in particular the phenoData slot for the
> datasets available. b
>
> On 31 August 2012 10:58, Jorge Miró <jorgma86 at gmail.com> wrote:
>> Hi everybody,
>>
>> I need to compare Student's t-test and the test implemented in the
>> limma package. Does any body has an idea of how I should do?
>>
>> I guess I need a data set with already known differentially expressed
>> genes (maybe this can be done by specially designing the probesets in
>> the used arrays?) and then compare the results of a t-tests and limma
>> test with the expected differentially expressed genes. Where can I get
>> such a data set?
>>
>> Sorry if the question is a bit stupid but I'm new to microarray
>> analysis and statistics... By the way, should this kind of questions
>> be posted here or should I use another forum?
>>
>>
>>
>> Best regards
>> Jorge
>>
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