[BioC] combine two microarray datasets based on affymatrix and cDNA array

[Sean Davis]

Hi, Avinash.

You might try the virtualArray package.  I have never used it, but it
aims to solve problems such as yours.

Sean


On Mon, Mar 11, 2013 at 1:08 AM, avinash sethi <avicct at gmail.com> wrote:
> 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 at 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 at 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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>
>