Question: affylmGUI segfault on "pd.ragene.1.0.st.v1"
0
gravatar for Harry Mangalam
10.9 years ago by
Harry Mangalam70 wrote:
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_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=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 -- Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, UC Irvine 92697 949 824-0084(o), 949 285-4487(c) --- Good judgment comes from experience; Experience comes from bad judgment. [F. Brooks.]
ADD COMMENTlink modified 10.9 years ago by Wolfgang Huber13k • written 10.9 years ago by Harry Mangalam70
Answer: affylmGUI segfault on "pd.ragene.1.0.st.v1"
0
gravatar for Wolfgang Huber
10.9 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k 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_COLLATE=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_IDEN TIFICATION=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 >
ADD COMMENTlink written 10.9 years ago by Wolfgang Huber13k
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. 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_COLLATE=en _US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=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 >> >
ADD REPLYlink written 10.9 years ago by Matt Settles70
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_COLLATE=e n_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_ID ENTIFICATION=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 >>> >> -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-5646 734-936-8662
ADD REPLYlink written 10.9 years ago by James W. MacDonald52k
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_COLLATE=e n_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_ID ENTIFICATION=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 >>> >> -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-5646 734-936-8662
ADD REPLYlink written 10.9 years ago by James W. MacDonald52k
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_COLLATE= 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_I DENTIFICATION=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 >>>> >>> >
ADD REPLYlink written 10.9 years ago by Matt Settles70
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_COLLATE =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 >>>>> >>>> >> -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-5646 734-936-8662
ADD REPLYlink written 10.9 years ago by James W. MacDonald52k
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 >>>>>> >>>>> >>> >
ADD REPLYlink written 10.9 years ago by Keith Satterley450
Hi Harry, 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. I don't know if/where the overview lives. It may not have made it onto the website as yet - perhaps Herve knows? > > > 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_COLLATE=en _US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=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 This sessionInfo is different than what you should get if you run the commands below. For instance, oligo isn't loaded. Additionally, you don't really want to load both oligo and affy, as they share some function names so you will end up with masking of things you will need, such as rma(). In other words, if you load oligo and then affylmGUI, the rma() that you will get comes from affy rather than oligo. So you are going to be unable to use affylmGUI to analyze these data, as this package assumes you are planning to use affy to do the normalization/summarization, and as you know this is done with oligo for these chips. So at this time your only recourse is to use the command-line tools in the oligo package. The segfault is irrelevant to this analysis, but hopefully Keith Satterley will see this thread (or you could contact him directly) in case you want to use affylmGUI for other analyses. Best, Jim >> ===== >> 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 >> > -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662
ADD REPLYlink written 10.9 years ago by James W. MacDonald52k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 179 users visited in the last hour