[BioC] Problems loading mraw

[Paquet, Agnes]

Hi Amy,

I haven't looked at the vignette you are using, so I will try to answer
your questions in a general way.

The error message " Error in inherits(x, "factor") : Object "mraw" not
found" means that the object "mraw" does not exist in your working
environment. You can check what objects are in your environment using
the command ls(). maQualityPlots takes as argument a marrayRaw or
marrayNorm object created for example using read.GenePix. In your case,
you will need to do something like:

mraw <- read.GenePix(fnames="TAMwithamp.gpr")
maQualityPlots(mraw)

This command will only read the file names TAMwithamp.gpr. If you want
to read in all gpr files that are in your working directory, you can for
example either not specify any file names:

mraw <- read.GenePix()

or specify all files names:
 
mraw <- read.GenePix(fnames=c("TAMnoamp.gpr", " TAMwithamp.gpr"))

"masked from package stats" means that the function "density" from
package "stats" is overwriting the "density" function in package
"mclust". It shouldn't be any problem here.

I hope this will help. If you have any other questions about
maQualityPlots, please let me know.

Regards,

Agnes


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Amy Mikhail
Sent: Monday, July 25, 2005 12:40 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Problems loading mraw

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)

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