[BioC] Problems loading mraw

[Amy Mikhail]

Dear all,

I am new to R and currently trying to follow some vignettes, swapping the
example files for my own data.

I am using R 2.1.0, Bioconductor I have downloaded from a CD provided at
the (recent) microarray analysis course in Bressanone, Italy.

I've been trying to work through various parts of the following vignettes:

(a) "Quick start guide for marray"
(b) "Introduction to the Bioconductor marray package: Input component"

So far I can import and read my files ok, but have had problems with the
the following:

> maQualityPlots(mraw)

I was originally getting a "colorspace not found" error message similar to
that of Naomi's post, so I downloaded the package from the website that
was indicated in one of her replies.

But now I'm getting a new error message:

> maQualityPlots(mraw)
Loading required package: hexbin
Loading required package: grid
Loading required package: colorspace

Attaching package: 'colorspace'


        The following object(s) are masked from package:grDevices :

         hcl

Error in inherits(x, "factor") : Object "mraw" not found

Does this mean there is something else I should download?  Would you
suggest I download all of bioconductor again, or just look for that
particular passage?

On a separate note, I did manage to create an image of my data but am
having a bit of trouble working out which slide it is coming from; I have
read in two .gpr files, "TAMnoamp.gpr" and "TAMwithamp.gpr":

> library("marray")
> dir(system.file("mossiedata",package="marray"))
[1] "MMC2_grid.gal"  "mossieData.txt" "TAMnoamp.gpr"   "TAMwithamp.gpr"
> datadir<-system.file("mossiedata",package="marray")
> setwd(datadir)
> mossiedataTargets<-read.marrayInfo(file.path(datadir,"mossieData.txt"))
> data<-read.GenePix(fnames="TAMnoamp.gpr")
Reading ...  TAMnoamp.gpr
> data<-read.GenePix(fnames="TAMwithamp.gpr")
Reading ...  TAMwithamp.gpr
> mossiedata.gnames<-read.marrayInfo(file.path(datadir,"MMC2_grid.gal"),
+ info.id=4:5,labels=5,skip=30)
> summary(mossiedata.gnames)
Object of class marrayInfo.

   maLabels   Name      ID
1   Cal. 01 cYIR01 Cal. 01
2   Cal. 04 cYIR04 Cal. 04
3   Cal. 07 cYIR07 Cal. 07
4   Cal. 10 cYIR10 Cal. 10
5   Cal. 01 cYIR01 Cal. 01
6   Cal. 04 cYIR04 Cal. 04
7   Cal. 07 cYIR07 Cal. 07
8   Cal. 10 cYIR10 Cal. 10
9   Cal. 03 cYIR03 Cal. 03
10  Cal. 05 cYIR05 Cal. 05
...

Number of labels:  13440
Dimensions of maInfo matrix:  13440  rows by  2  columns

Notes:
 C:/PROGRA~1/R/rw2010/library/marray/mossiedata/MMC2_grid.gal
> library(arrayQuality)
Loading required package: convert
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
         Vignettes contain introductory material.  To view,
         simply type: openVignette()
         For details on reading vignettes, see
         the openVignette help page.
[1] "arrayQuality"
[1] "Checking for missing packages"
Garbage collection 135 = 74+19+42 (level 2) ...
809344 cons cells free (67%)
15.1 Mbytes of heap free (78%)
[1] "Loading required packages"

Attaching package: 'mclust'


        The following object(s) are masked from package:stats :

         density

> image(data)
[1] FALSE
NULL

Does this mean that the image I get is from the second file only
(TAMwithamp.gpr) since that is the last one assigned to "data"?

Is there any way of writing titles on the graphs / objects (with this code
all that is written on the top of the image is ":image of M")?

Also what does "masked from package stats" mean?

Appologies for writing such a long post and asking so many questions...

Looking forward to any replies and suggestions,

Amy.

-------------------------------------------
Amy Mikhail
Research student
University of Aberdeen
Zoology Building
Tillydrone Avenue
Aberdeen AB24 2TZ
Scotland
Email: a.mikhail at abdn.ac.uk
Phone: 00-44-1224-272880 (lab)