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
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
> anal
(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
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$getReadablePath("plmData")
[1] "plmData"
Ok, and then the output of:
path <- getPath(plm)
print(path)
dir("plmData")
isDirectory("plmData")
Arguments$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-
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
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
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 <- AffymetrixCe
