Hello,
I have big agilent files to deal with and want to know if there is a
way to collapse them by reading them and writing out the maimages but
with the fields I am after.
The script I used to read them are as follows :
targets <- readTargets("TargetsTest.txt",sep="\t")
RG <- read.maimages(targets$FileName, source = "agilent",
names=targets$Description, columns= list(R = "rProcessedSignal", G =
"gProcessedSignal", Rb = "rBGUsed", Gb = "gBGUsed"), annotation = c("F
eatureNum","Row","Col","ProbeName","ControlType","GeneName","Descripti
on","SystematicName"))
there is no function called write.maimages but is there something
similar that would take the RG attributes and write them out so they
can be read later using read.maimages?
thanks
Dear Ruppert,
I think RGList objects are intended for further analysis, not for
exporting...
Do you want to collapse the individual files? I'd use a combination of
read.delim() and write.table() in a loop; see ?read.delim and its
colClasses
argument for specifying which columns to read.
Alternatively, for exporting the dataset as a whole, I'd try something
like
DF <- cbind(RG$genes, G = RG$G, Gb = RG$Gb, R = RG$R, Rb = RG$Rb)
write.table(DF, file = <filename>, sep = "\t", row,names = FALSE,
quote =
FALSE)
(almost untested :-))
Cheers,
- axel
Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
Switzerland
Ruppert Valentino
<ruppert7 at="" hotmail="" .com="">
To
Sent by: BioC
bioconductor-boun <bioconductor at="" stat.math.ethz.ch="">
ces at stat.math.eth
cc
z.ch
Subject
[BioC] Is there anyway I can
write
02.11.2009 14:41 out data similar to reading
them
using read.maimages?
Hello,
I have big agilent files to deal with and want to know if there is a
way to
collapse them by reading them and writing out the maimages but with
the
fields I am after.
The script I used to read them are as follows :
targets <- readTargets("TargetsTest.txt",sep="\t")
RG <- read.maimages(targets$FileName, source = "agilent",
names=targets$Description, columns= list(R = "rProcessedSignal", G =
"gProcessedSignal", Rb = "rBGUsed", Gb = "gBGUsed"), annotation =
c("FeatureNum","Row","Col","ProbeName","ControlType","GeneName","Descr
iption","SystematicName"))
there is no function called write.maimages but is there something
similar
that would take the RG attributes and write them out so they can be
read
later using read.maimages?
thanks
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Dear Ruppert,
There is no function like "write.maimages" because there's no need for
it.
limma reads only the columns it needs, which means that it reads
Agilent
files with many columns nearly as quickly as ones with just a few
columns.
Besides, I don't like to alter raw data files, just on principle. It
is
the number 1 way to introduce difficult to trace errors.
Best wishes
Gordon
> Date: Mon, 2 Nov 2009 13:41:38 +0000
> From: Ruppert Valentino <ruppert7 at="" hotmail.com="">
> Subject: [BioC] Is there anyway I can write out data similar to
> reading them using read.maimages?
> To: BioC <bioconductor at="" stat.math.ethz.ch="">
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
> Hello,
>
> I have big agilent files to deal with and want to know if there is a
way
> to collapse them by reading them and writing out the maimages but
with
> the fields I am after.
>
> The script I used to read them are as follows :
>
>
> targets <- readTargets("TargetsTest.txt",sep="\t")
>
> RG <- read.maimages(targets$FileName, source = "agilent",
> names=targets$Description, columns= list(R = "rProcessedSignal", G =
> "gProcessedSignal", Rb = "rBGUsed", Gb = "gBGUsed"), annotation =
> c("FeatureNum","Row","Col","ProbeName","ControlType","GeneName","Des
cription","SystematicName"))
>
>
> there is no function called write.maimages but is there something
> similar that would take the RG attributes and write them out so they
can
> be read later using read.maimages?
>
>
> thanks