[BioC] Problems loading mraw
Amy Mikhail
a.mikhail at abdn.ac.uk
Tue Jul 26 19:59:16 CEST 2005
Sorry, there was a typo in that last explanation - TAMnoamp has no
amplification step (obviously it was hybridised to the slide!)
Cheers,
Amy.
---------------------------------------------------------------------------
> 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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