[BioC] Problems loading mraw
Amy Mikhail
a.mikhail at abdn.ac.uk
Tue Jul 26 19:50:27 CEST 2005
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)
>
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