Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)
I've narrowed down this bug to the R.utils package and fixed it. I've verified that the RMA pipeline now also works running in /tmp/. Update aroma.affymetrix (including R.utils) by running: source("http://callr.org/install#aroma.affymetrix";) in a fresh R session. /Henrik On Tue, Sep 16, 2014 at 11:11 PM, jjspring OH wrote: > Finally working well after changing into one step further deeper directory > as your comment, > > Sunghee > > > 2014년 9월 17일 수요일 오후 3시 2분 20초 UTC+9, Henrik Bengtsson 님의 말: >> >> (Back to the public forum) >> >> REPRODUCIBLE EXAMPLE: >> It's a bug (still to be found) that shows itself when one runs the >> analysis in one directory up from the root /, e.g. /arom-anal/. I >> managed to reproduce this by running a standard analysis in /tmp/. >> >> WORKAROUND: >> Run the analysis in directory that is at least one step deeper, e.g. >> /foo/arom-anal/. The problem goes away when I run the analysis in >> /tmp/foo/. >> >> Please confirm that the above workaround also works for you and thanks >> for reporting on this. I'll fix the bug as soon as I can. >> >> /Henrik >> >> On Tue, Sep 16, 2014 at 10:52 PM, jjspring OH wrote: >> > >> > >> > yes it is working >> > >> >> >> >> Arguments$getReadablePath("plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1") >> > [1] "plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1" >> > >> > >> > Sunghee >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > Sunghee Oh, PhD >> > Director, Kim Sook Za Children's Hospital Medical Center Research >> > Foundation, >> > 745 JikJi Daero Heung Deok Gu >> > Cheng Ju City Chung Buk >> > 361-841, S. Korea >> > >> > >> > >> > >> > >> > >> > >> > >> > On Wed, Sep 17, 2014 at 2:48 PM, Henrik Bengtsson >> > >> > wrote: >> >> >> >> Let's continue this off the list to spare the others the noise and >> >> post back when we found the solution. >> >> >> >> Continuing, and before I'll have to dig into the low-level code to >> >> figure out why you possibly could get this weird problem, does >> >> >> >> >> >> Arguments$getReadablePath("plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1") >> >> >> >> work as well? >> >> >> >> /Henrik >> >> >> >> >> >> >> >> On Tue, Sep 16, 2014 at 10:40 PM, jjspring OH >> >> wrote: >> >> > >> >> > >> >> > >> >> > Hi Henrik, >> >> > >> >> > See the outputs: >> >> > >> >> >> path <- getPath(plm) >> >> >> print(path) >> >> > [1] "plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1" >> >> >> dir("plmData") >> >> > [1] "tissues,RBC,QN,RMA""tissues,RBC,QN,RMA,merged" >> >> >> isDirectory("plmData") >> >> > [1] TRUE >> >> >> Arguments$getReadablePath("plmData") >> >> > [1] "plmData" >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > 2014년 9월 17일 수요일 오후 2시 14분 45초 UTC+9, Henrik Bengtsson 님의 말: >> >> >> >> >> >> Ok, and then the output of: >> >> >> >> >> >> path <- getPath(plm) >> >> >> print(path) >> >> >> dir("plmData") >> >> >> isDirectory("plmData") >> >> >> Arguments$getReadablePath("plmData") >> >> >> >> >> >> /H >> >> >> >> >> >> >> >> >> On Tue, Sep 16, 2014 at 9:57 PM, jjspring OH >> >> >> wrote: >> >> >> > Hi Henrik, >> >> >> > >> >> >> > See below: >> >> >> > >> >> >> > >> >> >> >> print(plm) >> >> >> > RmaPlm: >> >> >> > Data set: tissues >> >> >> > Chip type: RaGene-1_0-st-v1,r3 >> >> >> > Input tags: RBC,QN >> >> >> > Output tags: RBC,QN,RMA >> >> >> > Parameters: {probeModel: chr "pm", shift: num 0, flavor: chr >> >> >> > "affyPLM", >> >> >> > treatNAsAs: chr "weights"} >> >> >> > Path: plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1 >> >> >> > RAM: 0.00MB >> >> >> >> print(getwd()) >> >> >> > [1] "/arom-anal" >> >> >> > >> >> >> > >> >> >> > Thanks >> >> >> > Sunghee >> >> >> > >> >> >> > >> >> >> > 2014년 9월 17일 수요일 오후 1시 45분 53초 UTC+9, Henrik Bengtsson 님의 말: >> >> >> >> >> >> >> >> That is really odd and I've never seen that error (8-9 years >> >> >> >> now). >> >> >> >> There must be a simple answer to this. What does: >> >> >> >> >> >> >> >> print(plm) >> >> >> >> print(getwd()) >> >> >> >> >> >> >> >> output when you get to that step. >> >> >> >> >> >> >> >> /Henrik >> >> >> >> >> >> >> >> >> >> >> >> On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH >> >> >> >> wrote: >> >> >> >> > >> >> >> >> > >> >> >> >> > Hi, >> >> >> >> > >> >> >> >> > After setting up the directory, performed background correction >> >> >> >> > and >> >> >> >> > rank >> >> >> >> > based quantile normalization, >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > library(aroma.affymetrix) >> >> >> >> > >> >> >> >> > verbose <- Arguments$getVerbose(-8, timestamp=T) >> >> >> >> > >> >> >> >> > chipType <- "RaGene-1_0-st-v1" >> >> >> >> > >> >> >> >> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3") >> >> >> >> > >> >> >> >> > cs <- AffymetrixCelSet$byName("tissues",cdf=cdf) >> >> >> >> > >> >> >> >> > >> >> >> >> > print(cs) >> >> >> >> > >> >> >> >> > >> >> >> >> >> cs >> >> >> >> > AffymetrixCelSet: >> >> >> >> > Name: tissues >> >> >> >> > Tags: >> >> >> >> > Pat
Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)
Finally working well after changing into one step further deeper directory as your comment, Sunghee 2014년 9월 17일 수요일 오후 3시 2분 20초 UTC+9, Henrik Bengtsson 님의 말: > > (Back to the public forum) > > REPRODUCIBLE EXAMPLE: > It's a bug (still to be found) that shows itself when one runs the > analysis in one directory up from the root /, e.g. /arom-anal/. I > managed to reproduce this by running a standard analysis in /tmp/. > > WORKAROUND: > Run the analysis in directory that is at least one step deeper, e.g. > /foo/arom-anal/. The problem goes away when I run the analysis in > /tmp/foo/. > > Please confirm that the above workaround also works for you and thanks > for reporting on this. I'll fix the bug as soon as I can. > > /Henrik > > On Tue, Sep 16, 2014 at 10:52 PM, jjspring OH > wrote: > > > > > > yes it is working > > > >> > Arguments$getReadablePath("plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1") > > [1] "plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1" > > > > > > Sunghee > > > > > > > > > > > > > > > > > > > > > > > > Sunghee Oh, PhD > > Director, Kim Sook Za Children's Hospital Medical Center Research > > Foundation, > > 745 JikJi Daero Heung Deok Gu > > Cheng Ju City Chung Buk > > 361-841, S. Korea > > > > > > > > > > > > > > > > > > On Wed, Sep 17, 2014 at 2:48 PM, Henrik Bengtsson > > > wrote: > >> > >> Let's continue this off the list to spare the others the noise and > >> post back when we found the solution. > >> > >> Continuing, and before I'll have to dig into the low-level code to > >> figure out why you possibly could get this weird problem, does > >> > >> > Arguments$getReadablePath("plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1") > >> > >> work as well? > >> > >> /Henrik > >> > >> > >> > >> On Tue, Sep 16, 2014 at 10:40 PM, jjspring OH > > >> wrote: > >> > > >> > > >> > > >> > Hi Henrik, > >> > > >> > See the outputs: > >> > > >> >> path <- getPath(plm) > >> >> print(path) > >> > [1] "plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1" > >> >> dir("plmData") > >> > [1] "tissues,RBC,QN,RMA""tissues,RBC,QN,RMA,merged" > >> >> isDirectory("plmData") > >> > [1] TRUE > >> >> Arguments$getReadablePath("plmData") > >> > [1] "plmData" > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > 2014년 9월 17일 수요일 오후 2시 14분 45초 UTC+9, Henrik Bengtsson 님의 말: > >> >> > >> >> Ok, and then the output of: > >> >> > >> >> path <- getPath(plm) > >> >> print(path) > >> >> dir("plmData") > >> >> isDirectory("plmData") > >> >> Arguments$getReadablePath("plmData") > >> >> > >> >> /H > >> >> > >> >> > >> >> On Tue, Sep 16, 2014 at 9:57 PM, jjspring OH > >> >> wrote: > >> >> > Hi Henrik, > >> >> > > >> >> > See below: > >> >> > > >> >> > > >> >> >> print(plm) > >> >> > RmaPlm: > >> >> > Data set: tissues > >> >> > Chip type: RaGene-1_0-st-v1,r3 > >> >> > Input tags: RBC,QN > >> >> > Output tags: RBC,QN,RMA > >> >> > Parameters: {probeModel: chr "pm", shift: num 0, flavor: chr > >> >> > "affyPLM", > >> >> > treatNAsAs: chr "weights"} > >> >> > Path: plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1 > >> >> > RAM: 0.00MB > >> >> >> print(getwd()) > >> >> > [1] "/arom-anal" > >> >> > > >> >> > > >> >> > Thanks > >> >> > Sunghee > >> >> > > >> >> > > >> >> > 2014년 9월 17일 수요일 오후 1시 45분 53초 UTC+9, Henrik Bengtsson 님의 말: > >> >> >> > >> >> >> That is really odd and I've never seen that error (8-9 years > now). > >> >> >> There must be a simple answer to this. What does: > >> >> >> > >> >> >> print(plm) > >> >> >> print(getwd()) > >> >> >> > >> >> >> output when you get to that step. > >> >> >> > >> >> >> /Henrik > >> >> >> > >> >> >> > >> >> >> On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH > > >> >> >> wrote: > >> >> >> > > >> >> >> > > >> >> >> > Hi, > >> >> >> > > >> >> >> > After setting up the directory, performed background correction > >> >> >> > and > >> >> >> > rank > >> >> >> > based quantile normalization, > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > library(aroma.affymetrix) > >> >> >> > > >> >> >> > verbose <- Arguments$getVerbose(-8, timestamp=T) > >> >> >> > > >> >> >> > chipType <- "RaGene-1_0-st-v1" > >> >> >> > > >> >> >> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3") > >> >> >> > > >> >> >> > cs <- AffymetrixCelSet$byName("tissues",cdf=cdf) > >> >> >> > > >> >> >> > > >> >> >> > print(cs) > >> >> >> > > >> >> >> > > >> >> >> >> cs > >> >> >> > AffymetrixCelSet: > >> >> >> > Name: tissues > >> >> >> > Tags: > >> >> >> > Path: ../../arom-anal/rawData/tissues/RaGene-1_0-st-v1 > >> >> >> > Platform: Affymetrix > >> >> >> > Chip type: RaGene-1_0-st-v1,r3 > >> >> >> > Number of arrays: 8 > >> >> >> > Names: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), > CS > >> >> >> > _ > >> >> >> > 7_(RaGene-1_0-st-v1), ..., NS _ 5_(RaGene-1_0-st-v1) [8] > >> >> >> > Time period:
Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)
(Back to the public forum) REPRODUCIBLE EXAMPLE: It's a bug (still to be found) that shows itself when one runs the analysis in one directory up from the root /, e.g. /arom-anal/. I managed to reproduce this by running a standard analysis in /tmp/. WORKAROUND: Run the analysis in directory that is at least one step deeper, e.g. /foo/arom-anal/. The problem goes away when I run the analysis in /tmp/foo/. Please confirm that the above workaround also works for you and thanks for reporting on this. I'll fix the bug as soon as I can. /Henrik On Tue, Sep 16, 2014 at 10:52 PM, jjspring OH wrote: > > > yes it is working > >> Arguments$getReadablePath("plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1") > [1] "plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1" > > > Sunghee > > > > > > > > > > > > Sunghee Oh, PhD > Director, Kim Sook Za Children's Hospital Medical Center Research > Foundation, > 745 JikJi Daero Heung Deok Gu > Cheng Ju City Chung Buk > 361-841, S. Korea > > > > > > > > > On Wed, Sep 17, 2014 at 2:48 PM, Henrik Bengtsson > wrote: >> >> Let's continue this off the list to spare the others the noise and >> post back when we found the solution. >> >> Continuing, and before I'll have to dig into the low-level code to >> figure out why you possibly could get this weird problem, does >> >> Arguments$getReadablePath("plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1") >> >> work as well? >> >> /Henrik >> >> >> >> On Tue, Sep 16, 2014 at 10:40 PM, jjspring OH >> wrote: >> > >> > >> > >> > Hi Henrik, >> > >> > See the outputs: >> > >> >> path <- getPath(plm) >> >> print(path) >> > [1] "plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1" >> >> dir("plmData") >> > [1] "tissues,RBC,QN,RMA""tissues,RBC,QN,RMA,merged" >> >> isDirectory("plmData") >> > [1] TRUE >> >> Arguments$getReadablePath("plmData") >> > [1] "plmData" >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > 2014년 9월 17일 수요일 오후 2시 14분 45초 UTC+9, Henrik Bengtsson 님의 말: >> >> >> >> Ok, and then the output of: >> >> >> >> path <- getPath(plm) >> >> print(path) >> >> dir("plmData") >> >> isDirectory("plmData") >> >> Arguments$getReadablePath("plmData") >> >> >> >> /H >> >> >> >> >> >> On Tue, Sep 16, 2014 at 9:57 PM, jjspring OH >> >> wrote: >> >> > Hi Henrik, >> >> > >> >> > See below: >> >> > >> >> > >> >> >> print(plm) >> >> > RmaPlm: >> >> > Data set: tissues >> >> > Chip type: RaGene-1_0-st-v1,r3 >> >> > Input tags: RBC,QN >> >> > Output tags: RBC,QN,RMA >> >> > Parameters: {probeModel: chr "pm", shift: num 0, flavor: chr >> >> > "affyPLM", >> >> > treatNAsAs: chr "weights"} >> >> > Path: plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1 >> >> > RAM: 0.00MB >> >> >> print(getwd()) >> >> > [1] "/arom-anal" >> >> > >> >> > >> >> > Thanks >> >> > Sunghee >> >> > >> >> > >> >> > 2014년 9월 17일 수요일 오후 1시 45분 53초 UTC+9, Henrik Bengtsson 님의 말: >> >> >> >> >> >> That is really odd and I've never seen that error (8-9 years now). >> >> >> There must be a simple answer to this. What does: >> >> >> >> >> >> print(plm) >> >> >> print(getwd()) >> >> >> >> >> >> output when you get to that step. >> >> >> >> >> >> /Henrik >> >> >> >> >> >> >> >> >> On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH >> >> >> wrote: >> >> >> > >> >> >> > >> >> >> > Hi, >> >> >> > >> >> >> > After setting up the directory, performed background correction >> >> >> > and >> >> >> > rank >> >> >> > based quantile normalization, >> >> >> > >> >> >> > >> >> >> > >> >> >> > library(aroma.affymetrix) >> >> >> > >> >> >> > verbose <- Arguments$getVerbose(-8, timestamp=T) >> >> >> > >> >> >> > chipType <- "RaGene-1_0-st-v1" >> >> >> > >> >> >> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3") >> >> >> > >> >> >> > cs <- AffymetrixCelSet$byName("tissues",cdf=cdf) >> >> >> > >> >> >> > >> >> >> > print(cs) >> >> >> > >> >> >> > >> >> >> >> cs >> >> >> > AffymetrixCelSet: >> >> >> > Name: tissues >> >> >> > Tags: >> >> >> > Path: ../../arom-anal/rawData/tissues/RaGene-1_0-st-v1 >> >> >> > Platform: Affymetrix >> >> >> > Chip type: RaGene-1_0-st-v1,r3 >> >> >> > Number of arrays: 8 >> >> >> > Names: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS >> >> >> > _ >> >> >> > 7_(RaGene-1_0-st-v1), ..., NS _ 5_(RaGene-1_0-st-v1) [8] >> >> >> > Time period: 2012-06-02 14:22:20 -- 2012-06-02 16:29:33 >> >> >> > Total file size: 84.50MB >> >> >> > RAM: 0.01MB >> >> >> > >> >> >> > >> >> >> > bc <- RmaBackgroundCorrection(cs) >> >> >> > >> >> >> > csBC <- process(bc,verbose=verbose) >> >> >> > >> >> >> > >> >> >> > >> >> >> > qn <- QuantileNormalization(csBC, typesToUpdate = "pm") >> >> >> > >> >> >> > print(qn) >> >> >> > >> >> >> > csN <- process(qn, verbose = verbose) >> >> >> > >> >> >> > plm <- RmaPlm(csN) >> >> >> > >> >> >> > print(plm) >> >> >> > >> >> >> > >> >> >> > >> >> >> > Until here, looks fine, BUT, when i perform fit function as below >> >> >> > and >> >> >> > the >> >> >> > errors come out related with directory, >> >> >> > >> >> >> > fit(plm, verbose = verbose) >> >> >>
Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)
Hi Henrik, See the outputs: > path <- getPath(plm) > print(path) [1] "plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1" > dir("plmData") [1] "tissues,RBC,QN,RMA""tissues,RBC,QN,RMA,merged" > isDirectory("plmData") [1] TRUE > Arguments$getReadablePath("plmData") [1] "plmData" 2014년 9월 17일 수요일 오후 2시 14분 45초 UTC+9, Henrik Bengtsson 님의 말: > > Ok, and then the output of: > > path <- getPath(plm) > print(path) > dir("plmData") > isDirectory("plmData") > Arguments$getReadablePath("plmData") > > /H > > > On Tue, Sep 16, 2014 at 9:57 PM, jjspring OH > wrote: > > Hi Henrik, > > > > See below: > > > > > >> print(plm) > > RmaPlm: > > Data set: tissues > > Chip type: RaGene-1_0-st-v1,r3 > > Input tags: RBC,QN > > Output tags: RBC,QN,RMA > > Parameters: {probeModel: chr "pm", shift: num 0, flavor: chr "affyPLM", > > treatNAsAs: chr "weights"} > > Path: plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1 > > RAM: 0.00MB > >> print(getwd()) > > [1] "/arom-anal" > > > > > > Thanks > > Sunghee > > > > > > 2014년 9월 17일 수요일 오후 1시 45분 53초 UTC+9, Henrik Bengtsson 님의 말: > >> > >> That is really odd and I've never seen that error (8-9 years now). > >> There must be a simple answer to this. What does: > >> > >> print(plm) > >> print(getwd()) > >> > >> output when you get to that step. > >> > >> /Henrik > >> > >> > >> On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH > wrote: > >> > > >> > > >> > Hi, > >> > > >> > After setting up the directory, performed background correction and > rank > >> > based quantile normalization, > >> > > >> > > >> > > >> > library(aroma.affymetrix) > >> > > >> > verbose <- Arguments$getVerbose(-8, timestamp=T) > >> > > >> > chipType <- "RaGene-1_0-st-v1" > >> > > >> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3") > >> > > >> > cs <- AffymetrixCelSet$byName("tissues",cdf=cdf) > >> > > >> > > >> > print(cs) > >> > > >> > > >> >> cs > >> > AffymetrixCelSet: > >> > Name: tissues > >> > Tags: > >> > Path: ../../arom-anal/rawData/tissues/RaGene-1_0-st-v1 > >> > Platform: Affymetrix > >> > Chip type: RaGene-1_0-st-v1,r3 > >> > Number of arrays: 8 > >> > Names: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _ > >> > 7_(RaGene-1_0-st-v1), ..., NS _ 5_(RaGene-1_0-st-v1) [8] > >> > Time period: 2012-06-02 14:22:20 -- 2012-06-02 16:29:33 > >> > Total file size: 84.50MB > >> > RAM: 0.01MB > >> > > >> > > >> > bc <- RmaBackgroundCorrection(cs) > >> > > >> > csBC <- process(bc,verbose=verbose) > >> > > >> > > >> > > >> > qn <- QuantileNormalization(csBC, typesToUpdate = "pm") > >> > > >> > print(qn) > >> > > >> > csN <- process(qn, verbose = verbose) > >> > > >> > plm <- RmaPlm(csN) > >> > > >> > print(plm) > >> > > >> > > >> > > >> > Until here, looks fine, BUT, when i perform fit function as below and > >> > the > >> > errors come out related with directory, > >> > > >> > fit(plm, verbose = verbose) > >> > > >> > qam <- QualityAssessmentModel(plm) > >> > > >> > #plotNuse(qam) > >> > > >> > plotRle(qam) > >> > > >> > > >> > > >> > current directory is /arom-anal, and setting up the data files > >> > (annotation, > >> > cel files, and raw data) look fine(see below hierarchical structure > of > >> > directories), > >> > After you take a closer look at the following errors, could you > please > >> > let > >> > me know what the problems are? > >> > > >> > > >> > > >> > Creating CEL file...done > >> > [2014-09-17 13:29:59] Exception: Pathname not found: > >> > > >> > > arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/probeAffinities.CEL > >> > (none of the parent directories > >> > [arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist; > current > >> > directory is '/arom-anal') > >> > > >> > at #22. getReadablePathname.Arguments(static, ...) > >> > - getReadablePathname.Arguments() is in environment > 'R.utils' > >> > > >> > at #21. getReadablePathname(static, ...) > >> > - getReadablePathname() is in environment 'R.utils' > >> > - originating from '' > >> > > >> > at #20. Arguments$getReadablePathname(filename, path = path, > >> > absolutePath > >> > = TRUE, > >> > mustExist = mustExist) > >> > - Arguments$getReadablePathname() is local of the calling > >> > function > >> > > >> > at #19. GenericDataFile(...) > >> > - GenericDataFile() is in environment 'R.filesets' > >> > > >> > at #18. extend(GenericDataFile(...), c("AromaMicroarrayDataFile", > >> > uses("FileCacheKeyInterface"))) > >> > - extend() is in environment 'R.oo' > >> > > >> > at #17. AromaMicroarrayDataFile(...) > >> > - AromaMicroarrayDataFile() is in environment 'aroma.core' > >> > > >> > at #16. extend(AromaMicroarrayDataFile(...), c("AffymetrixFile", > >> > uses("AromaPlatformInterface"))) > >> > - extend() is in environment 'R.oo'
Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)
Ok, and then the output of: path <- getPath(plm) print(path) dir("plmData") isDirectory("plmData") Arguments$getReadablePath("plmData") /H On Tue, Sep 16, 2014 at 9:57 PM, jjspring OH wrote: > Hi Henrik, > > See below: > > >> print(plm) > RmaPlm: > Data set: tissues > Chip type: RaGene-1_0-st-v1,r3 > Input tags: RBC,QN > Output tags: RBC,QN,RMA > Parameters: {probeModel: chr "pm", shift: num 0, flavor: chr "affyPLM", > treatNAsAs: chr "weights"} > Path: plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1 > RAM: 0.00MB >> print(getwd()) > [1] "/arom-anal" > > > Thanks > Sunghee > > > 2014년 9월 17일 수요일 오후 1시 45분 53초 UTC+9, Henrik Bengtsson 님의 말: >> >> That is really odd and I've never seen that error (8-9 years now). >> There must be a simple answer to this. What does: >> >> print(plm) >> print(getwd()) >> >> output when you get to that step. >> >> /Henrik >> >> >> On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH wrote: >> > >> > >> > Hi, >> > >> > After setting up the directory, performed background correction and rank >> > based quantile normalization, >> > >> > >> > >> > library(aroma.affymetrix) >> > >> > verbose <- Arguments$getVerbose(-8, timestamp=T) >> > >> > chipType <- "RaGene-1_0-st-v1" >> > >> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3") >> > >> > cs <- AffymetrixCelSet$byName("tissues",cdf=cdf) >> > >> > >> > print(cs) >> > >> > >> >> cs >> > AffymetrixCelSet: >> > Name: tissues >> > Tags: >> > Path: ../../arom-anal/rawData/tissues/RaGene-1_0-st-v1 >> > Platform: Affymetrix >> > Chip type: RaGene-1_0-st-v1,r3 >> > Number of arrays: 8 >> > Names: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _ >> > 7_(RaGene-1_0-st-v1), ..., NS _ 5_(RaGene-1_0-st-v1) [8] >> > Time period: 2012-06-02 14:22:20 -- 2012-06-02 16:29:33 >> > Total file size: 84.50MB >> > RAM: 0.01MB >> > >> > >> > bc <- RmaBackgroundCorrection(cs) >> > >> > csBC <- process(bc,verbose=verbose) >> > >> > >> > >> > qn <- QuantileNormalization(csBC, typesToUpdate = "pm") >> > >> > print(qn) >> > >> > csN <- process(qn, verbose = verbose) >> > >> > plm <- RmaPlm(csN) >> > >> > print(plm) >> > >> > >> > >> > Until here, looks fine, BUT, when i perform fit function as below and >> > the >> > errors come out related with directory, >> > >> > fit(plm, verbose = verbose) >> > >> > qam <- QualityAssessmentModel(plm) >> > >> > #plotNuse(qam) >> > >> > plotRle(qam) >> > >> > >> > >> > current directory is /arom-anal, and setting up the data files >> > (annotation, >> > cel files, and raw data) look fine(see below hierarchical structure of >> > directories), >> > After you take a closer look at the following errors, could you please >> > let >> > me know what the problems are? >> > >> > >> > >> > Creating CEL file...done >> > [2014-09-17 13:29:59] Exception: Pathname not found: >> > >> > arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/probeAffinities.CEL >> > (none of the parent directories >> > [arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist; current >> > directory is '/arom-anal') >> > >> > at #22. getReadablePathname.Arguments(static, ...) >> > - getReadablePathname.Arguments() is in environment 'R.utils' >> > >> > at #21. getReadablePathname(static, ...) >> > - getReadablePathname() is in environment 'R.utils' >> > - originating from '' >> > >> > at #20. Arguments$getReadablePathname(filename, path = path, >> > absolutePath >> > = TRUE, >> > mustExist = mustExist) >> > - Arguments$getReadablePathname() is local of the calling >> > function >> > >> > at #19. GenericDataFile(...) >> > - GenericDataFile() is in environment 'R.filesets' >> > >> > at #18. extend(GenericDataFile(...), c("AromaMicroarrayDataFile", >> > uses("FileCacheKeyInterface"))) >> > - extend() is in environment 'R.oo' >> > >> > at #17. AromaMicroarrayDataFile(...) >> > - AromaMicroarrayDataFile() is in environment 'aroma.core' >> > >> > at #16. extend(AromaMicroarrayDataFile(...), c("AffymetrixFile", >> > uses("AromaPlatformInterface"))) >> > - extend() is in environment 'R.oo' >> > >> > at #15. AffymetrixFile(...) >> > - AffymetrixFile() is in environment 'aroma.affymetrix' >> > >> > at #14. extend(AffymetrixFile(...), "AffymetrixCelFile", >> > `cached:.header` >> > = NULL, >> > `cached:.lastPlotData` = NULL, .cdf = NULL) >> > - extend() is in environment 'R.oo' >> > >> > at #13. AffymetrixCelFile(...) >> > - AffymetrixCelFile() is in environment 'aroma.affymetrix' >> > >> > at #12. extend(AffymetrixCelFile(...), c("ParameterCelFile", >> > uses("ParametersInterface")), >> > `cached:.readUnitsCache` = NULL, encodeFunction = >> > encodeFunction, >> > decodeFunction = decodeFunction) >> > - extend() is in environment 'R.oo' >> > >> > at #11. ParameterCelFile(...) >> > - ParameterCelFile() is in environment 'aroma.affymetrix' >> > >>
Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)
Hi Henrik, See below: > print(plm) RmaPlm: Data set: tissues Chip type: RaGene-1_0-st-v1,r3 Input tags: RBC,QN Output tags: RBC,QN,RMA Parameters: {probeModel: chr "pm", shift: num 0, flavor: chr "affyPLM", treatNAsAs: chr "weights"} Path: plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1 RAM: 0.00MB > print(getwd()) [1] "/arom-anal" Thanks Sunghee 2014년 9월 17일 수요일 오후 1시 45분 53초 UTC+9, Henrik Bengtsson 님의 말: > > That is really odd and I've never seen that error (8-9 years now). > There must be a simple answer to this. What does: > > print(plm) > print(getwd()) > > output when you get to that step. > > /Henrik > > > On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH > wrote: > > > > > > Hi, > > > > After setting up the directory, performed background correction and rank > > based quantile normalization, > > > > > > > > library(aroma.affymetrix) > > > > verbose <- Arguments$getVerbose(-8, timestamp=T) > > > > chipType <- "RaGene-1_0-st-v1" > > > > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3") > > > > cs <- AffymetrixCelSet$byName("tissues",cdf=cdf) > > > > > > print(cs) > > > > > >> cs > > AffymetrixCelSet: > > Name: tissues > > Tags: > > Path: ../../arom-anal/rawData/tissues/RaGene-1_0-st-v1 > > Platform: Affymetrix > > Chip type: RaGene-1_0-st-v1,r3 > > Number of arrays: 8 > > Names: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _ > > 7_(RaGene-1_0-st-v1), ..., NS _ 5_(RaGene-1_0-st-v1) [8] > > Time period: 2012-06-02 14:22:20 -- 2012-06-02 16:29:33 > > Total file size: 84.50MB > > RAM: 0.01MB > > > > > > bc <- RmaBackgroundCorrection(cs) > > > > csBC <- process(bc,verbose=verbose) > > > > > > > > qn <- QuantileNormalization(csBC, typesToUpdate = "pm") > > > > print(qn) > > > > csN <- process(qn, verbose = verbose) > > > > plm <- RmaPlm(csN) > > > > print(plm) > > > > > > > > Until here, looks fine, BUT, when i perform fit function as below and > the > > errors come out related with directory, > > > > fit(plm, verbose = verbose) > > > > qam <- QualityAssessmentModel(plm) > > > > #plotNuse(qam) > > > > plotRle(qam) > > > > > > > > current directory is /arom-anal, and setting up the data files > (annotation, > > cel files, and raw data) look fine(see below hierarchical structure of > > directories), > > After you take a closer look at the following errors, could you please > let > > me know what the problems are? > > > > > > > > Creating CEL file...done > > [2014-09-17 13:29:59] Exception: Pathname not found: > > > arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/probeAffinities.CEL > > (none of the parent directories > > [arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist; current > > directory is '/arom-anal') > > > > at #22. getReadablePathname.Arguments(static, ...) > > - getReadablePathname.Arguments() is in environment 'R.utils' > > > > at #21. getReadablePathname(static, ...) > > - getReadablePathname() is in environment 'R.utils' > > - originating from '' > > > > at #20. Arguments$getReadablePathname(filename, path = path, > absolutePath > > = TRUE, > > mustExist = mustExist) > > - Arguments$getReadablePathname() is local of the calling > function > > > > at #19. GenericDataFile(...) > > - GenericDataFile() is in environment 'R.filesets' > > > > at #18. extend(GenericDataFile(...), c("AromaMicroarrayDataFile", > > uses("FileCacheKeyInterface"))) > > - extend() is in environment 'R.oo' > > > > at #17. AromaMicroarrayDataFile(...) > > - AromaMicroarrayDataFile() is in environment 'aroma.core' > > > > at #16. extend(AromaMicroarrayDataFile(...), c("AffymetrixFile", > > uses("AromaPlatformInterface"))) > > - extend() is in environment 'R.oo' > > > > at #15. AffymetrixFile(...) > > - AffymetrixFile() is in environment 'aroma.affymetrix' > > > > at #14. extend(AffymetrixFile(...), "AffymetrixCelFile", > `cached:.header` > > = NULL, > > `cached:.lastPlotData` = NULL, .cdf = NULL) > > - extend() is in environment 'R.oo' > > > > at #13. AffymetrixCelFile(...) > > - AffymetrixCelFile() is in environment 'aroma.affymetrix' > > > > at #12. extend(AffymetrixCelFile(...), c("ParameterCelFile", > > uses("ParametersInterface")), > > `cached:.readUnitsCache` = NULL, encodeFunction = > > encodeFunction, > > decodeFunction = decodeFunction) > > - extend() is in environment 'R.oo' > > > > at #11. ParameterCelFile(...) > > - ParameterCelFile() is in environment 'aroma.affymetrix' > > > > at #10. extend(ParameterCelFile(...), "ProbeAffinityFile", > > `cached:.firstCells` = NULL, > > probeModel = probeModel) > > - extend() is in environment 'R.oo' > > > > at #09. this(...) > > - this() is in
Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)
That is really odd and I've never seen that error (8-9 years now). There must be a simple answer to this. What does: print(plm) print(getwd()) output when you get to that step. /Henrik On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH wrote: > > > Hi, > > After setting up the directory, performed background correction and rank > based quantile normalization, > > > > library(aroma.affymetrix) > > verbose <- Arguments$getVerbose(-8, timestamp=T) > > chipType <- "RaGene-1_0-st-v1" > > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3") > > cs <- AffymetrixCelSet$byName("tissues",cdf=cdf) > > > print(cs) > > >> cs > AffymetrixCelSet: > Name: tissues > Tags: > Path: ../../arom-anal/rawData/tissues/RaGene-1_0-st-v1 > Platform: Affymetrix > Chip type: RaGene-1_0-st-v1,r3 > Number of arrays: 8 > Names: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _ > 7_(RaGene-1_0-st-v1), ..., NS _ 5_(RaGene-1_0-st-v1) [8] > Time period: 2012-06-02 14:22:20 -- 2012-06-02 16:29:33 > Total file size: 84.50MB > RAM: 0.01MB > > > bc <- RmaBackgroundCorrection(cs) > > csBC <- process(bc,verbose=verbose) > > > > qn <- QuantileNormalization(csBC, typesToUpdate = "pm") > > print(qn) > > csN <- process(qn, verbose = verbose) > > plm <- RmaPlm(csN) > > print(plm) > > > > Until here, looks fine, BUT, when i perform fit function as below and the > errors come out related with directory, > > fit(plm, verbose = verbose) > > qam <- QualityAssessmentModel(plm) > > #plotNuse(qam) > > plotRle(qam) > > > > current directory is /arom-anal, and setting up the data files (annotation, > cel files, and raw data) look fine(see below hierarchical structure of > directories), > After you take a closer look at the following errors, could you please let > me know what the problems are? > > > > Creating CEL file...done > [2014-09-17 13:29:59] Exception: Pathname not found: > arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/probeAffinities.CEL > (none of the parent directories > [arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist; current > directory is '/arom-anal') > > at #22. getReadablePathname.Arguments(static, ...) > - getReadablePathname.Arguments() is in environment 'R.utils' > > at #21. getReadablePathname(static, ...) > - getReadablePathname() is in environment 'R.utils' > - originating from '' > > at #20. Arguments$getReadablePathname(filename, path = path, absolutePath > = TRUE, > mustExist = mustExist) > - Arguments$getReadablePathname() is local of the calling function > > at #19. GenericDataFile(...) > - GenericDataFile() is in environment 'R.filesets' > > at #18. extend(GenericDataFile(...), c("AromaMicroarrayDataFile", > uses("FileCacheKeyInterface"))) > - extend() is in environment 'R.oo' > > at #17. AromaMicroarrayDataFile(...) > - AromaMicroarrayDataFile() is in environment 'aroma.core' > > at #16. extend(AromaMicroarrayDataFile(...), c("AffymetrixFile", > uses("AromaPlatformInterface"))) > - extend() is in environment 'R.oo' > > at #15. AffymetrixFile(...) > - AffymetrixFile() is in environment 'aroma.affymetrix' > > at #14. extend(AffymetrixFile(...), "AffymetrixCelFile", `cached:.header` > = NULL, > `cached:.lastPlotData` = NULL, .cdf = NULL) > - extend() is in environment 'R.oo' > > at #13. AffymetrixCelFile(...) > - AffymetrixCelFile() is in environment 'aroma.affymetrix' > > at #12. extend(AffymetrixCelFile(...), c("ParameterCelFile", > uses("ParametersInterface")), > `cached:.readUnitsCache` = NULL, encodeFunction = > encodeFunction, > decodeFunction = decodeFunction) > - extend() is in environment 'R.oo' > > at #11. ParameterCelFile(...) > - ParameterCelFile() is in environment 'aroma.affymetrix' > > at #10. extend(ParameterCelFile(...), "ProbeAffinityFile", > `cached:.firstCells` = NULL, > probeModel = probeModel) > - extend() is in environment 'R.oo' > > at #09. this(...) > - this() is in environment 'aroma.affymetrix' > > at #08. newInstance.Class(.class, getPathname(paf), cdf = getCdf(ds), > probeModel = this$probeModel) > - newInstance.Class() is in environment 'R.oo' > > at #07. newInstance(.class, getPathname(paf), cdf = getCdf(ds), probeModel > = this$probeModel) > - newInstance() is in environment 'R.oo' > > at #06. getProbeAffinityFile.ProbeLevelModel(this, verbose = > less(verbose)) > - getProbeAffinityFile.ProbeLevelModel() is in environment > 'aroma.affymetrix' > > at #05. NextMethod("getProbeAffinityFile") > - NextMethod() is in environment 'base' > > at #04. getProbeAffinityFile.RmaPlm(this, verbose = less(verbose)) > - getProbeAffinityFile.RmaPlm() is in environment > 'aroma.affymetrix' > > at #03. getProbeAffinityFile(this, verbose = less(verbose)) > -