[BioC] Reading Agilent files using read.maimages

[Steve Taylor]

Hi Misha,

> 
> The files you downloaded from ArrayExpress are in fact in its own  
> format. For this experiment, in case you might find it useful, we  
> placed the original Agilent raw data files as given to us by the  
> submitter at ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/ 
> experiment/MEXP/E-MEXP-668/E-MEXP-668.original-raw-data.tar.gz.

Yes, that would have been useful to know. It would be nice if this was clearer in ArrayExpress, since it is confusing if you don't know the format...

Regards,

Steve

> 
> Hope this helps.
> 
> --Misha K.
> Microarray Informatics Team, EBI
> 
> On 16 Aug 2007, at 14:35, Steve Taylor wrote:
> 
>> Hi,
>>
>> I removed the prefixes from the file headers and they eventually  read 
>> in.
>>
>> I did get:
>>
>> Read ./E-MEXP-668-raw-data-921408043.txt
>> Read ./E-MEXP-668-raw-data-921408048.txt
>> Read ./E-MEXP-668-raw-data-921408053.txt
>> Read ./E-MEXP-668-raw-data-921408058.txt
>> Error in RG[[a]][, i] <- obj[, columns[[a]]] :
>>          number of items to replace is not a multiple of  replacement 
>> length
>>
>> which I think is due to inconsistent numbers of columns in some  files 
>> (and read.maimages doesn't seem to cope with), but I managed  to get 
>> round this by reording the targets file. I have got the data
>> to normalise now.
>>
>> Thank you all very much for helping me on this problem.
>>
>> Steve
>>
>>
>>> I have download the files and it seems that each file has its own
>>> header. By this I mean that a prefix has been add to each standard  
>>> column.
>>> For example, for file "E-MEXP-668-raw-data-921408043.txt" every  column
>>> start with "H_C1 A_mock A and B/" whereas in file
>>> "E-MEXP-668-raw-data-921408128.txt" it is "H_C52 B_mock A and B/". In
>>> order to make the read.maimages work you should remove those  
>>> prefixes. I
>>> have changed it for a couple of slides and it worked for me.
>>>
>>> targets <-read.("AE.csv", path=".",sep=",")
>>> RG <- read.maimages(targets$FileName[c 
>>> (1,16)]),path=".",source="agilent")
>>> Read ./E-MEXP-668-raw-data-921408043.txt
>>> Read ./E-MEXP-668-raw-data-921408118.txt
>>>
>>>> str(RG$G)
>>>
>>>
>>>  num [1:22153, 1:2] 960.4  73.1  83.3 648.1 132.9 ...
>>>  - attr(*, "dimnames")=List of 2
>>>   ..$ : NULL
>>>   ..$ : chr [1:2] "E-MEXP-668-raw-data-921408043"
>>> "E-MEXP-668-raw-data-921408118"
>>>
>>> Hope it helps,
>>> Nolwenn
>>>
>>> Scott Reagan Franklin wrote:
>>>
>>>> Steve:
>>>>
>>>> It should be noted that when you are using read.maimages with
>>>> source="agilent" and you are using the actual Agilent Raw Data file,
>>>> you will, by default, have RG$R and RG$G equal to the rMeanSignal  and
>>>> gMeanSignal.  In order to specify that they be equal to the
>>>> rProcessedSignal and gProcessedSignal you need to add an option to
>>>> read.maimages:
>>>>
>>>> RG<-read.maimages(targets$FileName,path=".",columns=list 
>>>> (R="rProcessedSignal",G="gProcessedSignal));
>>>>
>>>> You can also specify which background signal is used as well by
>>>> including in Rb and Gb in the list above.  By default Rb and Gb are
>>>> chosen as the median background signals.
>>>>
>>>