Thanks for the clarification with that,
When I try to open up the arrayExplorer in firefox nothing seems to
load, under unix this is the error i'm getting:
Error: cannot open display:
When I took a look in the spatial file directory there were no files
there, which I believe is what the problem would be?
I was just following the codes from the Vignette: HUman exon array
anaysis (Human exon array)
Thanks in advance for any suggestions
-K
Here's my code if its of help:
library(aroma.affymetrix)
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
cdf<-AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2") #cdf file name
should be the same as the chipType
print(cdf)
####AffymetrixCdfFile:
Path: annotationData/chipTypes/HuEx-1_0-st-v2
Filename: HuEx-1_0-st-v2.CDF
Filesize: 305.88MB
Chip type: HuEx-1_0-st-v2
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 1432154
Cells per unit: 4.58
Number of QC units: 0#####
cs<-AffymetrixCelSet$byName("Control", chipType="HuEx-1_0-st-v2")
#####AffymetrixCelSet:
Name: Control
Tags:
Path: rawData/Control/HuEx-1_0-st-v2
Platform: Affymetrix
Chip type: HuEx-1_0-st-v2
Number of arrays: 4
Names: HuEx1_0028, HuEx1_0028, HuEx1_0035, HuEx1_0035
Time period: 2010-09-28 19:06:17 -- 2010-09-28 19:37:21
Total file size: 255.97MB
RAM: 0.01MB #####
setCdf(cs, cdf)
bc <- RmaBackgroundCorrection(cs, tag="coreR2")
csBC <- process(bc,verbose=verbose)
qn <- QuantileNormalization(csBC, typesToUpdate="pm")
csN <- process(qn, verbose=verbose)
getCdf(csN)
plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
print(plmTr)
plmEx <- ExonRmaPlm(csN, mergeGroups=FALSE)
fit(plmTr, verbose=verbose)
rs <- calculateResiduals(plmTr, verbose=verbose)
ae <- ArrayExplorer(rs)
setColorMaps(ae, c("log2,log2neg,rainbow", "log2,log2pos,rainbow"))
process(ae, interleaved="auto", verbose=verbose)
display(ae)
###Error: cannot open display: [server domain name]:0 ###
On Dec 2, 11:41 pm, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> Hi.
>
> On Wed, Dec 1, 2010 at 4:08 PM, kraman <kripa...@hotmail.com> wrote:
> > Hi, I'm new to microarray analysis and aroma.affymetrix
> > I'm trying to create a dynamic report, output using arrayexplorer but
> > i'm getting this error:
>
> > Warning messages:
> > 1: In is.na(x) : is.na() applied to non-(list or vector) of type
> > 'NULL'
> > 2: In writeImages.SpatialReporter(reporter, arrays = arrays, aliases =
> > aliases, :
> > No color maps specified. Nothing to do.
> > 3: In is.na(x) : is.na() applied to non-(list or vector) of type
> > 'NULL'
>
> Nothing to worry about. Everything should work as expected.
>
> Those are *warnings* not *errors*. In R, there is a strict difference
> between the two. Typically when you get an *error*, the R
> function/script stops, whereas with a *warning* everything continues.
> Compare:
>
> > log("a")
>
> Error in log("a") : Non-numeric argument to mathematical function
>
> and
>
> > log(-1)
>
> [1] NaN
> Warning message:
> In log(-1) : NaNs produced
>
>
>
>
>
> > I'm trying to analyze huex chips. This is a summary of my code thus
> > far if it's of any help:
>
> > cdf<-AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2")
>
> > cs<-AffymetrixCelSet$byName("Control", chipType="HuEx-1_0-st-v2")
>
> > qn<- QuantileNormalization(cs)
> > csN <- process(qn)
>
> > plm<- RmaPlm(csN)
> > fit(plm)
> > ces<- getChipEffectSet(plm)
>
> > rs<-calculateResidualSet(plm)
> > ae<-ArrayExplorer(rs)
> > process(ae) ###this is where i see the error
>
> So if this keeps running, which I think it did for you, because
> normally warnings are only displayed when everything is finished.
>
> Have a look at the directory ./reports/Control/<some tags>/ and you
> should see a file ArrayExplorer.html. Look in its subdirectories and
> you should see large PNG files containing the spatial plots. Open
> that in Firefox(!). Alternatively, you could also try display(ae) if
> your default browser is Firefox.
>
> /Henrik
>
>
>
> > Any suggestions would be greatly appreciated!!
> > Thanks
>
> > -K
>
> > --
> > When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> > version of the package, 2) to report the output of sessionInfo() and
> > traceback(), and 3) to post a complete code example.
>
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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