[BioC] Reading Agilent files using read.maimages

[Steve Taylor]

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.
>>
>>
>>  
>