[BioC] Limma - GenePix

[john seers (IFR)]

Hi Juan

If you look at the code for read.maimages there appear to be four
entries for genepix:


genepix = ,    (Not sure what this does).

genepix.mean = list(R = "F635 Mean", G = "F532 Mean", Rb = "B635
Median", Gb = "B532 Median"), 
         
genepix.median = list(R = "F635 Median", G = "F532 Median", Rb = "B635
Median", Gb = "B532 Median"), 

genepix.custom = list(R = "F635 Mean", G = "F532 Mean", Rb = "B635", Gb
= "B532"),



Your code columns are 

Rf="GenePix:F635Mean",
Gf="GenePix:F532 Mean",
Rb="GenePix:B635 Median",
Gb="GenePix:B532 Median")


which nearly match the genepix.mean entry. (I don't think you need the
"GenePix:" in each entry. Also perhaps "R" and "G", not "Rf", and "Gf").

Regards


John


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Juana Arco
Sent: 23 June 2009 14:53
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Limma - GenePix


 
	
	

Hi,
Can
anybody help me with this?
1)
I've
downloaded from the ArrayExpress some GenePix files that don't have
headers. Because of that I had to read the files (.txt extension for
some reason) this way:

RG <-
read.maimages(targets$Filename, columns=list(Rf="GenePix:F635
Mean",Gf="GenePix:F532 Mean",Rb="GenePix:B635
Median",Gb="GenePix:B532 Median"), sep="\t",
path="./")

Is this correct?

2) I had to
create the targets files from a file provided by arrayexpress which
looked something like this:



SlideNumber	Source
Name	Label	FileName
1	8CT	Cy5	1348628744.txt
2	5Exp	Cy3	1348628729.txt
3	10Exp	Cy5	1348628754.txt
4	4CT	Cy3	1348628724.txt
5	1Exp	Cy5	1348628709.txt
6	12Exp	Cy5	1348628764.txt
7	6Exp	Cy5	1348628734.txt
8	3CT	Cy3	1348628719.txt
9	13Exp	Cy3	1348628769.txt
10	7Exp	Cy3	1348628739.txt
11	2CT	Cy5	1348628714.txt
12	11Exp	Cy3	1348628759.txt
13	9Exp	Cy5	1348628749.txt
14	14CT	Cy3	1348628774.txt



And
my target file looks like this



SlideNumber	Filename	Cy3	Cy5
1	1348628744.txt	case	control
2	1348628729.txt	case	control
3	1348628754.txt	control	case
4	1348628724.txt	control	case
5	1348628709.txt	control	case
6	1348628764.txt	control	case
7	1348628734.txt	control	case
8	1348628719.txt	control	case
9	1348628769.txt	case	control
10	1348628739.txt	case	control
11	1348628714.txt	case	control
12	1348628759.txt	case	control
13	1348628749.txt	control	case
14	1348628774.txt	control	case

Is
this correct?
Luana

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