[BioC] read.maimages in limma package

[john seers (IFR)]

Hi Giusy



>1. list with fields R, G, Rb and Gb giving the column names to be used
>for red and green foreground and background;

As already discussed.

>2. character vector of names of other columns to be read containing
>spot-specific information;

Use other.names= parameter of read.maimages. I have not used this so I
cannot say any more. 

>3. character vector of names of columns containing annotation
>information about the probes;

Use the annotation= parameter of read.maimages to set the annotation
columns. No file involved unless I have misunderstood you.



Looking at your previous email more closely I am a bit puzzled as it
looks like you may have read one array (Read Control_2b.txt) in
successfully. If so it must have standard Agilent column names. Perhaps
your second array file has a problem?


>Read Control_2b.txt
>Read Control_3b.txt
>Error in readGenericHeader(fullname, columns = columns) :
>Specified column headings not found in file 

Regards


John (or is it Peter) Seers

 
---
-----Original Message-----
From: Giusy Della Gatta [mailto:Gatta at icg.cpmc.columbia.edu] 
Sent: 17 December 2008 13:25
To: john seers (IFR); bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] read.maimages in limma package

Thank you Peter,

I'll check it out!
I have also seen that I have to make a file
in which I have to describe agilent 
annotations (see point 3 of my previuos email).

May you know where I have to check to retrieve 
informations on the file format that I have to use?

Thank you 
G


-----Original Message-----
From: john seers (IFR) [mailto:john.seers at bbsrc.ac.uk]
Sent: Wed 12/17/2008 4:36 AM
To: Giusy Della Gatta; bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] read.maimages in limma package
 
Hi Giusy

If you look at the code for read.maimages you can see which columns
limma is expecting for agilent:

agilent = list(G = "gMeanSignal", 
            Gb = "gBGMedianSignal", R = "rMeanSignal", Rb =
"rBGMedianSignal"),


If your custom arrays do not match these names then you have to specify
them yourself (using the columns parameter of read.maimages).





Regards

John Seers

 
---



Hi!
I am analyzing custom two color agilent array by using limma package and
I am having some problems with the read.maimages
comand:

I launch this comand:

> read.maimages("Targets$Filename, source="agilent")

and the error that I have is the following:

Read Control_2b.txt
Read Control_3b.txt
Error in readGenericHeader(fullname, columns = columns) :
Specified column headings not found in file

It is like the columns in the file that I gave as input (Control_.txt)
are not recognized,
maybe I have this problem because is a custom agilent array?

If this is the problem, I have to specify in my script the following
informations:

1. list with fields R, G, Rb and Gb giving the column names to be used
for red and green foreground and background;
2. character vector of names of other columns to be read containing
spot-specific information;
3. character vector of names of columns containing annotation
information about the probes;

Is there someone that can answer me and that has got some experience in
the 
two color agilent custom array analysis?


Thank you in advance
Giusy

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor