Hi
This is an R- problem and I have seen it crop up in R mailing list. Please
check there.
-Best
-Lax
On Fri, May 15, 2009 at 11:23 AM, chunjiang he <camel...@gmail.com> wrote:
> Hi,
>
> Thanks again. Now the path is OK and it is no problem until the
> image creating.
>
> When I library(EBImage), I got the following error:
>
> > library(EBImage)
> Error in inDL(x, as.logical(local), as.logical(now), ...) :
> unable to load shared library
> 'D:/PROGRA~2/R/R-29~1.0/library/EBImage/libs/EBImage.dll':
> LoadLibrary failure: The specified module could not be found.
>
> Error: package/namespace load failed for 'EBImage'
>
> I found the file in
> D:\Program Files (x86)\R\R-2.9.0\library\EBImage\libs\EBImage.dll
>
> and I have installed *ImageMagick* and GTK+ Runtime Environment in
> default directory. My OS is vista x64. How can I deal with this problem.
>
> Best,
> jiang
>
>
> On Thu, May 14, 2009 at 3:36 PM, Lakshmanan Iyer <lax...@gmail.com> wrote:
>
>> Hi
>> If you change the working directory to the proper one under which you have
>> put all these directories and files, and source the script from there it
>> should automatically recognize it and work fine. Give it a spin and tell me
>> what you get.
>>
>> As for patient answers, others have done more for my ignorance!
>> My only hope is that I am not misleading you :-)
>> -Best
>> -Lax
>>
>>
>>
>> On Thu, May 14, 2009 at 4:21 PM, chunjiang he <camel...@gmail.com> wrote:
>>
>>> Thanks so much for the patient answers.
>>>
>>> I think there are some problems with my environment path. I have put all
>>> my data and CDF in directories strictly as yours. But the problem is also
>>> the same. I checked my CDF files.
>>> I put 5 files in the /annotationData/chipTypes/MoGene-1_0-st-v1:
>>>
>>> MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
>>> MoEx-1_0-st-v1,extendedR1,A20080718,MR.cdf
>>> MoEx-1_0-st-v1,fullR1,A20080718,MR.cdf
>>> MoEx-1_0-st-v1,U-Ensembl50,G-Affy,EP.cdf
>>> MoEx-1_0-st-v1.cdf
>>>
>>> I think the *,monocell.cdf may be created automatically when I run the
>>> scripts.
>>>
>>> And i put all the CEL files in /rawData/JunXu/MoGene-1_0-st-v1. So I
>>> think it is no problem. But does the script can recognize the path
>>> automatically, or I must indicate it in R scripts?
>>> On Thu, May 14, 2009 at 2:38 PM, Lakshmanan Iyer <lax...@gmail.com>wrote:
>>>
>>>> Hi
>>>> Put the raw data, CEL files in,
>>>> C:/Documents and Settings/rawData/JunXu/MoGene-1_0-st-v1
>>>>
>>>> and annotatino file, CDF files, in
>>>> C:/Documents and Settings/annotationData/chipTypes/MoGene-1_0-st-v1
>>>>
>>>> Copy the R-script below in note book and save it as "myscript.R"
>>>>
>>>> Now Launch R
>>>> Change Working directory to C:/Documents and Settings
>>>> use the R command:
>>>> source ("myscript.R")
>>>> to execute the commands and it should work.
>>>>
>>>> I am afraid, I am making this up from my previous experience working
>>>> with PCs.
>>>>
>>>> -Best
>>>> -Lax
>>>>
>>>>
>>>> On Thu, May 14, 2009 at 3:00 PM, chunjiang he <camel...@gmail.com>wrote:
>>>>
>>>>> Thanks very much,
>>>>> But how could I set my data path and array path in windows. I mean how
>>>>> to set it when I use R.
>>>>> when I run this:
>>>>>
>>>>> > cdf<-AffymetrixCdfFile$fromChipType(chipType)
>>>>>
>>>>> I got the error:
>>>>>
>>>>> Error in list(`AffymetrixCdfFile$fromChipType(chipType)` =
>>>>> <environment>, :
>>>>>
>>>>> [2009-05-14 13:57:50] Exception: Could not locate a file for this chip
>>>>> type: MoGene-1_0-st-v1
>>>>> at throw(Exception(...))
>>>>> at throw.default("Could not locate a file for this chip type: ",
>>>>> paste(c(chipT
>>>>> at throw("Could not locate a file for this chip type: ",
>>>>> paste(c(chipType, tag
>>>>> at byChipType.UnitNamesFile(static, ...)
>>>>> at byChipType(static, ...)
>>>>> at method(static, ...)
>>>>> at AffymetrixCdfFile$fromChipType(chipType)
>>>>>
>>>>> Best,
>>>>> Jiang
>>>>>
>>>>> On Thu, May 14, 2009 at 12:45 PM, Lakshmanan Iyer
>>>>> <lax...@gmail.com>wrote:
>>>>>
>>>>>> Hi,
>>>>>> Hope this helps!
>>>>>> Here is how I ran a Affy, MoGene-1_0-st chip analysis on a
>>>>>> ubuntu/linux box:
>>>>>> Please double check the code to make sure that it is fine! I have not
>>>>>> looked at it for a long time.
>>>>>> -Best
>>>>>> -Lax
>>>>>> ________________________________________________________________
>>>>>> The CEL file (JC1.CEL JC2.CEL NC1.CEL NC2.CEL) are in:
>>>>>> /home/laxman/Projects/Analysis/rawData/JunXu/MoGene-1_0-st-v1
>>>>>>
>>>>>> The annotation files, CDF files, (MoGene-1_0-st-v1.cdf
>>>>>> MoGene-1_0-st-v1,monocell.CDF) are in:
>>>>>>
>>>>>> /home/laxman/Projects/Analysis/annotationData/chipTypes/MoGene-1_0-st-v1
>>>>>>
>>>>>> Directory in which I am running the jobs. Contains the R script file,
>>>>>> see below:
>>>>>> /home/laxman/Projects/Analysis
>>>>>> Pay attention to the line following: #<<<<<<<<<<<<<<<<<
>>>>>>
>>>>>> The results would be found in:
>>>>>> /home/laxman/Projects/Analysis/Results/JunXu
>>>>>>
>>>>>> #####################################################################
>>>>>> # Script to calculate probeset level/gene level intensities
>>>>>> #Based on
>>>>>> http://groups.google.com/group/aroma-affymetrix/web/human-exon-array-analysis
>>>>>> #Load the library
>>>>>> library(aroma.affymetrix)
>>>>>> verbose <- Arguments$getVerbose(-8)
>>>>>> timestampOn(verbose)
>>>>>> #
>>>>>> #<<<<<<<<<<<<<<<<<
>>>>>> #setup the CDF explicitly as:
>>>>>> chipType <- "MoGene-1_0-st-v1"
>>>>>> cdf <- AffymetrixCdfFile$fromChipType(chipType)
>>>>>> #
>>>>>> #Next we setup the CEL set with the above custom CDF:
>>>>>> ##<<<<<<<<<<<<
>>>>>> cs <- AffymetrixCelSet$fromName("JunXu", cdf=cdf)
>>>>>> setCdf(cs,cdf)
>>>>>> #
>>>>>> #In order to do RMA background correction, we setup a correction
>>>>>> method and runs it by:
>>>>>> #
>>>>>> bc <- RmaBackgroundCorrection(cs)
>>>>>> csBC <- process(bc,verbose=verbose)
>>>>>> #Note that this is the first step where we will create new files,
>>>>>> #so we have put in a tag that should follow through the rest of the
>>>>>> analysis.
>>>>>> #
>>>>>> #We then setup a quantile normalization method:
>>>>>> qn <- QuantileNormalization(csBC, typesToUpdate="pm")
>>>>>> print(qn)
>>>>>> #
>>>>>> #and we then run it by:
>>>>>> csN <- process(qn, verbose=verbose)
>>>>>> print (csN)
>>>>>> #
>>>>>> #You can check associated CSF with the command
>>>>>> getCdf(csN)
>>>>>> #
>>>>>> #To fit a summary of the entire transcript (i.e. estimate the overall
>>>>>> expression for the transcript), do
>>>>>> plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
>>>>>> print(plmTr)
>>>>>> #
>>>>>> #Otherwise, to fit exon-by-exon, change the value of mergeGroups to
>>>>>> FALSE in the ExonRmaPlm() call above.
>>>>>> #
>>>>>> # plmEx <- ExonRmaPlm(csN, mergeGroups=FALSE)
>>>>>> # print(plmEx)
>>>>>> #
>>>>>> #To fit the PLM to all of the data, do:
>>>>>> #
>>>>>> fit(plmTr, verbose=verbose)
>>>>>> #
>>>>>> #or similarly for plmEx.
>>>>>> # fit(plmEx, verbose=verbose)
>>>>>> #
>>>>>> #Quality assessment of PLM fit
>>>>>> #
>>>>>> #To calculate the residuals from the PLM fit, do:
>>>>>> #
>>>>>> rs <- calculateResiduals(plmTr, verbose=verbose)
>>>>>> #
>>>>>> #To browse spatial false-colored images of the residuals, do:
>>>>>> ae <- ArrayExplorer(rs)
>>>>>> setColorMaps(ae, c("log2,log2neg,rainbow",
>>>>>> "log2,log2pos,rainbow"))
>>>>>> process(ae, interleaved="auto", verbose=verbose)
>>>>>> # display(ae)
>>>>>> #
>>>>>> #To examine NUSE and RLE plots, do
>>>>>> #Note that this can be done to fits based on the transcript level
>>>>>> #or exon level depending on which plm you chose and can give different
>>>>>> interpretations.
>>>>>> qamTr <- QualityAssessmentModel(plmTr)
>>>>>> # save plots in pdf file
>>>>>> pdf(file="/home/laxman/Projects/Analysis/Results/JunXu/NusePlot.pdf");
>>>>>> plotNuse(qamTr)
>>>>>> pdf(file="/home/laxman/Projects/Analysis/Results/JunXu/RlePlot.pdf");
>>>>>> plotRle(qamTr)
>>>>>> dev.off()
>>>>>> # turned pdf off
>>>>>> #
>>>>>> #
>>>>>> #To extract the estimates (transcript or probeset)
>>>>>> #use either extractMatrix() or extractDataFrame() on the ChipEffectSet
>>>>>> that corresponds to the plm object:
>>>>>> #This will give a data.frame with three rows, each row corresponding
>>>>>> to a unit/transcript
>>>>>> #
>>>>>> cesTr <- getChipEffectSet(plmTr)
>>>>>> trFit <- extractDataFrame(cesTr, addNames=TRUE)
>>>>>> write.table
>>>>>> (trFit[,c(1,6:9)],"/home/laxman/Projects/Analysis/Results/JunXu/trFit.tsv",
>>>>>> sep="\t", quote=F)
>>>>>>
>>>>>> #
>>>>>> #To get estimates of the probesets/exons
>>>>>> #you must choose mergeGroups=FALSE as described
>>>>>> #above when you define your plm object, and then extract the estimates
>>>>>> from it.
>>>>>> #
>>>>>> # cesEx <- getChipEffectSet(plmEx)
>>>>>> # exFit <- extractDataFrame(cesEx,units=1:3,addNames=TRUE)
>>>>>> #
>>>>>> #Alternative Splicing Analysis (FIRMA)
>>>>>> firma <- FirmaModel(plmTr)
>>>>>> fit(firma, verbose=verbose)
>>>>>> fs <- getFirmaScores(firma)
>>>>>> x <- extractDataFrame(fs)
>>>>>>
>>>>>> On Thu, May 14, 2009 at 12:25 PM, chunjiang he <camel...@gmail.com>wrote:
>>>>>>
>>>>>>> Hi all,
>>>>>>> I am sorry I cannot understand the path of data directory of
>>>>>>> aroma.affymetrix. Such as
>>>>>>>
>>>>>>> annotationData/chipTypes/<chip type>/
>>>>>>>
>>>>>>> what does this sentence mean? where I can put mouse CDF files? I am
>>>>>>> using windows vista.
>>>>>>>
>>>>>>> And what is the following mean:
>>>>>>>
>>>>>>>
>>>>>>> <data set path> = <path>/<data set name>(,tag)*/
>>>>>>> <array set path> = <data set path>/<chip type>/
>>>>>>>
>>>>>>> where I can set them?
>>>>>>>
>>>>>>> Thanks very much.
>>>>>>>
>>>>>>> jiang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>> >>
>>
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