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. > > > You received this message because you are subscribed to the Google Groups > > "aroma.affymetrix" group with websitehttp://www.aroma-project.org/. > > To post to this group, send email to aroma-affymetrix@googlegroups.com > > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/ -- 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. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/