Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

2014-09-17 Thread Henrik Bengtsson
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)

2014-09-16 Thread jjspring OH
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)

2014-09-16 Thread Henrik Bengtsson
(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)

2014-09-16 Thread jjspring OH



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)

2014-09-16 Thread Henrik Bengtsson
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)

2014-09-16 Thread jjspring OH
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)

2014-09-16 Thread Henrik Bengtsson
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))
>   -