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))
> -
