One dataset is from ATH1-affymatrix genechip and another from cDNA-array.
Each dataset has 4 biological replicates at each time point (0hpi,24hpi).
In total, there are 8 and 4 assays from above two platform respectively.
In cDNA-array, common reference was labeled with Cy3 and Cy5 was used to
label 0hpi or 24 hpi.
I want to integrate these two datasets at raw intensity level and then do
downstream analysis (normalization, batch effect removal, differential
expression).
-array


On Mon, Mar 11, 2013 at 2:02 AM, Sean Davis <seandavi@gmail.com> wrote:

> What is the experimental design on the two platforms?  What comparisons do
> you want to make?
> On Mar 10, 2013 1:57 PM, "Avinash [guest]" <guest@bioconductor.org> wrote:
>
>>
>> Hi,
>> I am trying to intermingle two timeseries expression data from two
>> different platform (affymatrix and cDNA array).To follow a common index
>> system, I mapped the probesets and cDNA clones (from above given platforms,
>> respectively) to unique entrez Ids. Only common Ids are retained (~7500).
>> How can I integrate or compare these two datasets together at intensity
>> level?
>>
>>
>>  -- output of sessionInfo():
>>
>>
>> R version 2.15.2 (2012-10-26)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> locale:
>>  [1] LC_CTYPE=en_US.UTF-8    LC_NUMERIC=C            LC_TIME=en_IN
>>  [4] LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_IN
>> LC_MESSAGES=en_US.UTF-8
>>  [7] LC_PAPER=C              LC_NAME=C               LC_ADDRESS=C
>> [10] LC_TELEPHONE=C          LC_MEASUREMENT=en_IN    LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>

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