[BioC] controls in mArray

[M Inmaculada Barrasa]

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,
id="Name")

because my identifiers are in Name column.

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


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

When I have a control code like this:

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

It doesnt see alien9 or alien10, but it sees:

HUMPPARP1+/-5'
HUMPPARP1+/-


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.

Inma