[BioC] bugs in arrayQuality and marray

[Paquet, Agnes]

Dear Francois,

Thank you very much for reporting these problems, I will try to fix them
as soon as possible. 

I have never noticed the weird spatial plots you are mentioning on my
test slides; could you please send me the file you are using so that I
can see what is going on?

Regards,

Agnes

-----Original Message-----
From: Francois Pepin [mailto:fpepin at cs.mcgill.ca] 
Sent: Friday, December 02, 2005 4:06 PM
To: BioClist
Cc: Paquet, Agnes; Jean Yee Hwa Yang
Subject: bugs in arrayQuality and marray

Hi everyone,

I've hit a couple of bugs while trying out arrayQuality (downloaded from
ucsf site, they have an earlier version than bioconductor) for my
Agilent arrays.

read.Agilent, from the marray package, is ignoring the 'path' parameter
when 'fnames' is given:

    if (is.null(fnames)) {
	...
    }
    else fullnames <- fnames



The readAgilent function, from the arrayQuality package, has problems
with the skip parameter. First of all, it is completely ignored:

   skip <- grep("gMedianSignal", y)[1]

Then lower down, it is incorrectly offset by +1:

    dat <- scan(f, quiet = TRUE, what = h, sep = sep, skip = skip +
        1, quote = quote, ...)

which means that the first gene is skipped (which then cause problems
because dimensions are not of the same).

Then maPrintTip in marray is confused with how Agilent probes are
positioned and seems to think that there are twice as many probes as
there are. Doing a print tip-based normalization doesn't make much sense
in this case (only 1 print tip is present), but it did end up making the
code crash. This can be fixed by specifying norm='l' (if loess
normalization is wanted) in the agQuality.

I think that should be the default in agQuality and change (in
agQuality):
        defs <- list(norm = "p")
to 
        defs <- list(norm = "l")

As a note, the diagnostic spatial images being produced are not correct
either. It produces 4 copies of the image rather than a single one. I've
attached a the output from a truly horrible array we have where it's
obvious. I assume this is again due to the awkward way Agilent has to
place its spots.

> sessionInfo()
R version 2.2.0, 2005-10-06, x86_64-redhat-linux-gnu

attached base packages:
[1] "grid"      "tools"     "methods"   "stats"     "graphics"
"grDevices"
[7] "utils"     "datasets"  "base"


other attached packages:
arrayQuality RColorBrewer     gridBase       hexbin   colorspace
convert
     "1.6.2"      "0.2-3"      "0.4-1"      "1.4.0"        "0.9"
"1.4.0"
     Biobase       marray        limma
     "1.8.0"      "1.8.0"      "2.3.7"


Francois