[BioC] Combining data from different versions of Illumina HumanHT-12 v3

[Gavin Koh]

Thank you Wei, I agree with your opinion, but can you help with the
technical details of how to do this, please? Gavin.

On 15 April 2011 02:38, Wei Shi <shi at wehi.edu.au> wrote:
> Hi Gavin:
>
>        The number of probes which were present in one batch but not in others should be very small. So you can use the probes which are common in all batches for your analysis.
>
>        Hope this helps.
>
> Cheers,
> Wei
>
> On Apr 15, 2011, at 1:20 AM, Gavin Koh wrote:
>
>> I am trying to analyse data from ArrayExpress E-GEOD-22098 (published
>> Dec last year).
>> According to the study methods, the data are Illumina HumanHT-12 v3
>> Expression BeadChips, but the hybridisation seems to have been done in
>> several batches, with different numbers of probes in each batch,
>> alternating between 48803 and 48804. Can anyone tell me how to combine
>> these different batches into the same file, please? I am trying to
>> read the probe data using the read.ilmn() function in limma, but
>> failing, because cbind complains the matrices are not the same length
>> (precise error is "Error in cbind(out$E, objects[[i]]$E) : number of
>> rows of matrices must match (see arg 2)").
>>
>> Thank you in advance,
>>
>> Gavin Koh
>>
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