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

[Gavin Koh]

Dear Wei,

Thank you for replying so quickly. There appear to be 6 batches in
this dataset (TB1 to 6)

> TB1$genes[1:10]
 [1] "ILMN_1809034" "ILMN_1660305" "ILMN_1792173" "ILMN_1762337"
"ILMN_2055271" "ILMN_1736007" "ILMN_1814316"
 [8] "ILMN_2359168" "ILMN_1731507" "ILMN_1787689"
> TB2$genes[1:10]
 [1] "ILMN_1762337" "ILMN_2055271" "ILMN_1736007" "ILMN_2383229"
"ILMN_1806310" "ILMN_1779670" "ILMN_2321282"
 [8] "ILMN_1671474" "ILMN_1772582" "ILMN_1735698"
> TB3$genes[1:10]
 [1] "ILMN_1809034" "ILMN_1660305" "ILMN_1792173" "ILMN_1762337"
"ILMN_2055271" "ILMN_1736007" "ILMN_1814316"
 [8] "ILMN_2359168" "ILMN_1731507" "ILMN_1787689"
> TB4$genes[1:10]
 [1] "ILMN_1762337" "ILMN_2055271" "ILMN_1736007" "ILMN_2383229"
"ILMN_1806310" "ILMN_1779670" "ILMN_2321282"
 [8] "ILMN_1671474" "ILMN_1772582" "ILMN_1735698"
> TB5$genes[1:10]
 [1] "ILMN_1809034" "ILMN_1660305" "ILMN_1792173" "ILMN_1762337"
"ILMN_2055271" "ILMN_1736007" "ILMN_1814316"
 [8] "ILMN_2359168" "ILMN_1731507" "ILMN_1787689"
> TB6$genes[1:10]
 [1] "ILMN_1762337" "ILMN_2055271" "ILMN_1736007" "ILMN_2383229"
"ILMN_1806310" "ILMN_1779670" "ILMN_2321282"
 [8] "ILMN_1671474" "ILMN_1772582" "ILMN_1735698"

多謝謝您的幫助！

Gavin

On 15 April 2011 11:45, Wei Shi <shi at wehi.edu.au> wrote:
> Hi Gavin:
>
>        It would be best if you can match the two batches using the probe identifiers because they are much less likely to have duplicates. Would it possible to show the first several probes in each dataset so that I can write some code to help you do this?
>
> Cheers,
> Wei
>
>
> On Apr 15, 2011, at 7:54 PM, Gavin Koh wrote:
>
>> 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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>>>
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>>
>>
>>
>> --
>> Hofstadter's Law: It always takes longer than you expect, even when
>> you take into account Hofstadter's Law.
>> —Douglas Hofstadter (in Gödel, Escher, Bach, 1979)
>
>
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