[BioC] Reading Agilent files using read.maimages

[Nolwenn LeMeur]

Hi 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.
>
>
>   


-- 
--
Nolwenn Le Meur, PhD.
Computational Biology, Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N., M2-876
P.O. Box 19024
Seattle, WA 98109-1024
Tel. (206) 667-5434