Hi
I am working on aroma.affymetrix package,
btw, it seems like i set up the annotationDat and rawData directory under
the current working directory(/arom-anal) right,
but not working when i upload cdf file with cdf <-
AffymetrixCdfFile$byChipType(chipType, tags="r3")
Please see my sessionInfo(
Hi,
After setting up the directory, performed background correction and rank
based quantile normalization,
library(aroma.affymetrix)
verbose <- Arguments$getVerbose(-8, timestamp=T)
chipType <- "RaGene-1_0-st-v1"
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")
cs <- AffymetrixCe
:
>
> print(plm)
> print(getwd())
>
> output when you get to that step.
>
> /Henrik
>
>
> On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH > wrote:
> >
> >
> > Hi,
> >
> > After setting up the directory, performed backgr
;)
[1] TRUE
> Arguments$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("
way 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:
> >
Hi,
I am getting errors when i run aroma.affymetrix package for dynamic
reports, it looks like for low level analysis, everything works well for
now,
Could you please take a closer look at and let me know what the problem is?
I am running under the current directory(/foo/arom-anal/)
> proce
p://cran.r-project.org’
6: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
Many Thanks!
Sunghee
2014년 9월 20일 토요일 오후 7시 58분 39초 UTC+9, jjspring OH 님의 말:
>
>
>
>
> Thanks Henrik,
>
> Yes, There is no error message on the command line display(a
Hi,
I would like to compare the results from plmTr and plmEx, estimation of
overall expression for transcripts and exon-by-exon estimation,
but when i tried to run ExonRmaPlm with mergeGroups = T and F,
respectively, i am getting the identical results for following objects
including FIRMA sc
And one more question:
On the FIRMA scores, what are NA values, though expression levels are not
zero?
Thanks,
Sunghee
2014년 9월 22일 월요일 오전 10시 50분 25초 UTC+9, jjspring OH 님의 말:
>
>
>
> Hi,
>
>
> I would like to compare the results from plmTr and plmEx, est
