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

[Gavin Koh]

Dear Wei,

A little more information: the difference seems to be a single duplicated probe.
Just comparing two batches (TB1 and TB2) with different probe numbers:
> length(TB1$genes)
[1] 48804
> length(TB2$genes)
[1] 48803
> length(unique(TB2$genes))
[1] 48803
> length(unique(TB1$genes))
[1] 48803
> setdiff(TB1$genes,TB2$genes)
character(0)
> setequal(TB1$genes,TB2$genes)
[1] TRUE

That still leaves me the problem that I don't know how to identify the
repeated probe or how to cbind TB1 and TB2... :-(

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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