Hi Amy,
There is an extra space in the 2nd file name, that's why it's not
found.
You should use something like"
mraw <- read.GenePix(fnames=c("TAMnoamp.gpr", "TAMwithamp.gpr"))
The error you are getting in maQualityPlots happens sometimes when
control spots are not defined properly. By default, they are set to
the
control spots we use in my lab.
You can check arrayQuality user guide for instructions about how to
set
up your own controls. You can also refer to help files for maControls
and maGenControls in the marray package.
There are several ways to set up your controls. The easiest way is to
set the R object controlCode to your own controls using
readcontrolCode(), and then read in your files and generate the
quality
plots.
If this doesn't work, could you please send me one of your gpr files
and
a spot type file (a tab-delimited text file containing your controls
types) so that I can fix the error?
Cheers,
Agnes
-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Amy
Mikhail
Sent: Tuesday, July 26, 2005 10:50 AM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Problems loading mraw
Hi Agnes,
When I carry out the list function this is what is in my environment:
> ls()
[1] "data" "datadir" "last.warning"
[4] "lymphenoData" "mossiedata.gnames" "mossiedataTargets"
[7] "mraw" "path"
I tried all three of your suggestions for reading in mraw - the first
two
worked {> mraw <- read.GenePix(fnames="TAMwithamp.gpr") and
> mraw <- read.GenePix()} but with the third option I get an error
message:
> mraw <- read.GenePix(fnames=c("TAMnoamp.gpr", " TAMwithamp.gpr"))
Reading ... TAMnoamp.gpr
Reading ... TAMwithamp.gpr
Error in file(con, "r") : unable to open connection
In addition: Warning message:
cannot open file ' TAMwithamp.gpr'
Why would there now be a problem opening "TAMwithamp.gpr" when it
worked
with the other two methods?
Also unfortunately I still can't get maQuality plots to work. This is
what happens when I try:
> maQualityPlots(mraw)
Error in seq.default(0, 1, length = min(17, maxcnt)) :
length must be non-negative number
In addition: Warning message:
no finite arguments to max; returning -Inf
What does this mean? Is there data missing?
FYI, both of these slides are tests - self hybridisations from two
colour
arrays, i.e. we were hoping for lots of yellow spots if everything
worked.
The first one (TAMnoamp.gpr) is where the sample was prepared without
a
hybridisation step - actually the signal is pretty awful with the
majority
of spots flagged "bad", so I would not have been quite so surprised if
the
above error message had appeared for this file.
For the second slide (TAMwithamp.gpr) the probe was prepared with an
amplification step and the resulting signal is much, much better, also
no
spots were flagged as "bad". So what's the error message referring
to?
Cheers,
Amy.
----------------------------------------------------------------------
--
---
> 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)
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
>
https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
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