[BioC] controls in mArray

M Inmaculada Barrasa ibarrasa at mail.med.upenn.edu
Thu Nov 11 20:01:22 CET 2004

Hi all,

Sorry if this is a basic thing that I am not seeing.

I have looking again and again at this but
I dont know what is going on here,
I am trying to read my controls into my ma Layout, and look if it is
reading them properly.

These are the commands I am using:

I am using read.GenePix()  to read gpr files.
I made my controlCode with:
controlCode <- as.matrix(read.table("controls.txt", sep="\t",header=TRUE,
quote="\"", fill=TRUE))

I am trying to put my controls in maLayout, by doing:
maControls(testRapa at maLayout) <- maGenControls(Raw at maGnames@maInfo,

because my identifiers are in Name column.

Some of the genes I have in my name column are
 alien9, alien 10, HUMPPARP1+/-5'

I dont have HUMPPARP1NC as an identifier in my Name columns.

When I have a control code like this:

  Pattern       Name
1 "alien9"      "con"
2 "alien10"     "con"
3 "HUMPPARP1NC" "con"

It doesnt see alien9 or alien10, but it sees:


When my control code is:

  Pattern        Name
1 "alien9"       "con"
2 "alien10"      "con"
3 "HUMPPARP1+/-" "con"

It doesnt label any of those genes as controls, even if they are there

I have created controls.txt with Xmacs and with excel. I dont think that
there are spaces in the names that may be doing that.

Any suggestions?

Thanks a lot.


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