Thanks Jim for the suggestions. I have been on leave for 2 weeks and will be back at work on Jan 12th. (Just popped in to read a few emails!). I will follow up on your point that affylmGUI should support the newer affy chips. I'll discuss this with Gordon Smyth next week and let the list know what we intend to do, cheers, Keith ======================== Keith Satterley (Maintainer of affylmGUI) Bioinformatics Division The Walter and Eliza Hall Institute of Medical Research Parkville, Melbourne, Victoria, Australia ======================= James W. MacDonald wrote: > Hi Matt, > > The problem as I see it is that affylmGUI is specifically designed to > work with either the affy, gcrma or affyPLM packages and the S4 > structures produced by those packages. So while you could try to make it > so an end user could load oligo after e.g., the affy package and thereby > mask all of the exposed functions from affy so they could then use > affylmGUI with oligo and fool it into using oligo's functions, I just > don't see the point. > > For instance, one could theoretically load affylmGUI, then oligo, and > the rma() function from oligo would mask that from affy. Then when you > try to normalize the data and affylmGUI calls rma() you would get the > oligo version, which presumably would then work correctly with the data > at hand. > > However, I think it is preferable that the maintainer of affylmGUI would > decide of his own volition to support the newer affy chips and directly > incorporate the functionality rather than modifying oligo so an end user > could theoretically trick the package into using oligo. > > Best, > > Jim > > Matt Settles wrote: >> James, >> >> Wouldn't that depend on how the information is accessed? If affylmgui >> uses functions for ALL its data access from the cdf env, then I could >> create functions in oligo that return the requested information in the >> expected form regardless of the underlying data structure. If >> affylmgui accesses the data directly with assumed data types then your >> absolutely correct and any changes would need to be made by that >> group. I don't know which is the case, but I would be very interested >> to know. >> >> One of my goals with these chip types in oligo is to be able to >> provide interface functions similar to what people are already used to >> with affy,, when appropriate, and hence better interoperability with >> existing packages. >> >> James W. MacDonald wrote: >>> Hi Matt, >>> >>> Matt Settles wrote: >>>> Harry, Wolfgang and James, >>>> >>>> The exon and gene ST arrays do not use, or even have, a CDF file for >>>> the array, I think a requirement for makecdfenv. These arrays use >>>> clf and pgf files, hence the need for the oligo set of packages. >>>> >>>> You can try changing the name of pd.ragene.1.0.st.v to >>>> ragene10stv1cdf then reinstalling. This should at least enable you >>>> to load the package within affylmgui, there may be errors when >>>> affylmgui tries to access the information in the package and I would >>>> be interested in what they are. I can then work on updating oligo to >>>> add an interface similar to what the affylmgui is expecting. >>> >>> I don't think that will be helpful. The pdInfo packages are based on >>> an underlying SQLite database whereas the cdfenvs are environment >>> based. Simply renaming something to look compatible and then trying >>> to use it will not work. >>> >>> And affylmGUI is expecting to use the affy package (hence the name), >>> so you won't be able to add anything to oligo that will help. Any >>> changes will have to occur in affylmGUI (or oligolmGUI if Keith >>> Satterley wants a new project ;-D). >>> >>> Best, >>> >>> Jim >>> >>>> >>>> Matt >>>> >>>> >>>> Wolfgang Huber wrote: >>>>> >>>>> Hi Harry & Matt >>>>> >>>>> re your second question, about the CDF package: the way the affy >>>>> package works, it expects a package with name "ragene10stv1cdf", >>>>> containing an R-environment of that same name, with the probeset >>>>> definitions for that chip. >>>>> >>>>> Note that the CDF packages that the "affy" package uses are *not* >>>>> the same as the platform design packages that the "oligo" package >>>>> uses. >>>>> Essentially: affy = old, tried and tested, but only works for >>>>> convential Affymetrix genechips for mRNA analysis with genechip >>>>> using 3' probe sets. >>>>> oligo = newer, more general, also suitable for more recent chip >>>>> types inclduding for genotyping.. >>>>> >>>>> It seems that you want affy and CDF packages. The make.cdf.package >>>>> function from the makecdfenv package is what you or Matt would want >>>>> to use to build these. >>>>> >>>>> Jim McDonald (cc-ed) has written an overview over the software >>>>> tools for analysing Affymetrix arrays, unfortunately I could not >>>>> figure out how to find it from the Bioconductor webpage, so maybe >>>>> he can help with that. >>>>> >>>>> >>>>> Best wishes >>>>> Wolfgang >>>>> >>>>> Harry Mangalam ha scritto: >>>>>> Hi All, >>>>>> >>>>>> I've been trying to get affylmGUI to run on my laptop (3GB, Ubuntu >>>>>> 8.04, R as below: >>>>>> ===== >>>>>>> sessionInfo() >>>>>> R version 2.8.0 (2008-10-20) >>>>>> i686-pc-linux-gnu >>>>>> >>>>>> locale: >>>>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLAT E=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF -8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC _IDENTIFICATION=C >>>>>> >>>>>> >>>>>> attached base packages: >>>>>> [1] tools tcltk stats graphics grDevices utils >>>>>> datasets >>>>>> [8] methods base >>>>>> >>>>>> other attached packages: >>>>>> [1] affylmGUI_1.16.0 affy_1.16.0 preprocessCore_1.0.0 >>>>>> [4] affyio_1.6.1 Biobase_2.2.1 limma_2.16.3 >>>>>> ===== >>>>>> The commands to start affylmGUI are: >>>>>> library("pd.ragene.1.0.st.v1") # the array set, from Matt Settles >>>>>> library("oligo") >>>>>> library("affylmGUI") >>>>>> affylmGUI() >>>>>> >>>>>> when I try to load data, whether my own (or the estrogen data >>>>>> set), it segfaults at the same place: >>>>>> After I select a working directory, and select the targets file >>>>>> (included below), [R churns for a few seconds], and give the new >>>>>> data set a name, I can see that the data is 'available' via the >>>>>> data tree in the left panel. >>>>>> >>>>>> At the point where I try to view the RNA targets via Menu -> RNA >>>>>> Targets -> RNA Targets, and release the mouse button, it >>>>>> segfaults, leaving the traceback: >>>>>> >>>>>> http://moo.nac.uci.edu/~hjm/affylmGUI.traceback >>>>>> >>>>>> As I said above, this is the case if it's my data or the estrogen >>>>>> data set. >>>>>> >>>>>> If I try to bypass that step and go direct to normalization (with >>>>>> my data), it will eventually emit the error that I don't have the >>>>>> correct CDF environment: >>>>>> >>>>>> ==== Error message ==== >>>>>> Error in getCdfInfo(object): Could not obtain CDF environment, >>>>>> problems encountered: Specified environment does not contain >>>>>> RaGene-1_0-st-v1 Library - package ragene10stv1cdf not installed. >>>>>> Data for package affy did not contain ragene10stv1cdf Bioconductor >>>>>> - ragene10stv1cdf not available >>>>>> ======================= >>>>>> >>>>>> This despite loading without error the correct (from Matt Settles) >>>>>> library beforehand. > library("pd.ragene.1.0.st.v1") >>>>>> Does the spelling variant muck it up? Best wishes, >>>>>> harry >>>>>> >>>>>> >>>>>> ==== targets.txt (whitespaces are TABS) ==== >>>>>> >>>>>> Name FileName Target >>>>>> AB.1 0908F-02_AB_1.CEL AB_Only >>>>>> AB.2 0908F-02_AB_2.CEL AB_Only >>>>>> AB.3 0908F-02_AB_3.CEL AB_Only >>>>>> CIQ.1 0908F-02_CIQ_1.CEL CIQ_Only >>>>>> CIQ.2 0908F-02_CIQ_2.CEL CIQ_Only >>>>>> CIQ.3 0908F-02_CIQ_3.CEL CIQ_Only >>>>>> CIQ+AB.1 0908F-02_CIQ_AB_1.CEL CIQ_AB_CoTreatment >>>>>> CIQ+AB.2 0908F-02_CIQ_AB_2.CEL CIQ_AB_CoTreatment >>>>>> CIQ+AB.3 0908F-02_CIQ_AB_3.CEL CIQ_AB_CoTreatment >>>>>> Untreated.1 0908F-02_Untreated_1.CEL CONTROL >>>>>> Untreated.2 0908F-02_Untreated_2.CEL CONTROL >>>>>> Untreated.3 0908F-02_Untreated_3.CEL CONTROL >>>>>> >>>>> >>> >