Hi Henrik,
I ran the script as explained in the 'Paired total copy number
analysis' . The script runs fine all the way,however, I wasnot able to
get raw CN estimates for both chiptypes. When I print cesFlnList, I
get result for only one of the chiptype.
> cesFlnList
$Mapping50K_Xba240
CnChipEffectSet:
Name: katia-TumorNormal1
Tags: ACC,-XY,RMA,+300,A+B,FLN,-XY
Path: plmData/katia-TumorNormal1,ACC,-XY,RMA,+300,A+B,FLN,-XY/
Mapping50K_Xba240
Platform: Affymetrix
Chip type: Mapping50K_Xba240,monocell
Number of arrays: 16
Names: TLL_ALL_10SA_REM, TLL_ALL_10SA, ..., TLL_ALL_9AM
Time period: 2008-10-29 23:36:31 -- 2008-10-29 23:36:33
Am I doing something wrong now?
Here is my script:
library(aroma.affymetrix)
log <- Arguments$getVerbose(-8)
timestampOn(verbose)
dataSetName <- "katia-TumorNormal1"
chipTypes <- c("Mapping50K_Hind240", "Mapping50K_Xba240")
pairs <- matrix(c(
"TLL_ALL_10SA_REM","TLL_ALL_10SA",
"TLL_ALL_13BP_REM","TLL_ALL_13BP",
"TLL_ALL_1BD_REM","TLL_ALL_1BD",
"TLL_ALL_2NP_REM","TLL_ALL_2NP",
"TLL_ALL_3MM_REM","TLL_ALL_3MM",
"TLL_ALL_5NL_REM","TLL_ALL_5NL",
"TLL_ALL_6TA_REM","TLL_ALL_6TA",
"TLL_ALL_9AM_REM","TLL_ALL_9AM"
),ncol=2,byrow=TRUE)
colnames(pairs) <- c("normal", "tumor")
#processing samples:
csRawList <- list()
for(chipType in chipTypes){
cs <- AffymetrixCelSet
$fromName(dataSetName,checkChipType=FALSE,chipType=chipType)
stopifnot(all(getNames(cs) %in% pairs))
csRawList[[chipType]]<- cs
}
print(csRawList)
#allellic crosstalk
csAccList <- list();
for(chiptype in names (csRawList)){
cs <- csRawList[[chipType]]
acc <- AllelicCrosstalkCalibration(cs)
print(acc)
csAcc<- process(acc, verbose=log)
csAccList[[chipType]]<- csAcc
}
#Summarization
cesList<- list()
for(chipType in names (csAccList)){
cs <- csAccList[[chipType]]
plm <- RmaCnPlm(cs, mergeStrands=TRUE, combineAlleles=TRUE,shift=+300)
print(plm)
fit(plm, verbose=log)
ces <- getChipEffectSet(plm)
cesList[[chipType]]<- ces
}
#PCR fragment length normalization
cesFlnList<- list()
for(chipType in names(cesList)){
ces <- cesList[[chipType]]
fln <- FragmentLengthNormalization(ces)
print(fln)
cesFln<- process(fln,verbose=log)
cesFlnList[[chiptype]]<- cesFln
}
Also, I tried the other method of running the steps given above for
each chip seperately. It runs fine for both chiptypes
Mapping50K_Hind240, Mapping50K_Xba240 , and seperate directories are
created for each chiptype under plmData and probeData , except that
the final object cesFlnList shows results for only one chiptype.
Is this right?
Please help! Thanks
On Oct 27, 5:33 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote:
> Hi,
>
> the mistake you are doing is that you tell R/aroma.affymetrix to
> process both chip types, but you only have/load data for one of them.
> You do:
>
> chipTypes <- c("Mapping50K_Hind240", "Mapping50K_Xba240")
>
> and this is what is used in the for loops. If you only want to
> process one of the chip types, the simplest modification you can do to
> solve the problem is to replace the above with:
>
> chipTypes <- "Mapping50K_Hind240"
>
> I recommend that you read up a bit more on R - it'll help
> troubleshoot/detect these problems. In the meanwhile, I've updated
> the Vignette 'Paired total copy number analysis' to be robust against
> this kind of mistakes.
>
> Cheers
>
> Henrik
>
>
>
> On Sat, Oct 25, 2008 at 2:05 PM,biobee<[EMAIL PROTECTED]> wrote:
>
> > Hi Henrik,
>
> > I checked and my csAccList[[chipType]] returns NULL. However chipTypes
> > is not empty. It reurns the following:
> >> chipTypes
> > [1] "Mapping50K_Hind240" "Mapping50K_Xba240"
>
> > Also my csAccList gives the following output:
> >> csAccList
> > $Mapping50K_Hind240
> > AffymetrixCelSet:
> > Name: katia-TumorNormal1
> > Tags: ACC,-XY
> > Path: probeData/katia-TumorNormal1,ACC,-XY/Mapping50K_Hind240
> > Platform: Affymetrix
> > Chip type: Mapping50K_Hind240
> > Number of arrays: 16
> > Names: TLL_ALL_10SA, TLL_ALL_10SA_REM, ..., TLL_ALL_9AM_REM
> > Time period: 2007-04-27 12:59:07 -- 2007-11-13 14:42:59
> > Total file size: 391.64MB
> > RAM: 0.02MB
>
> >>csAcc
> > AffymetrixCelSet:
> > Name: katia-TumorNormal1
> > Tags: ACC,-XY
> > Path: probeData/katia-TumorNormal1,ACC,-XY/Mapping50K_Hind240
> > Platform: Affymetrix
> > Chip type: Mapping50K_Hind240
> > Number of arrays: 16
> > Names: TLL_ALL_10SA, TLL_ALL_10SA_REM, ..., TLL_ALL_9AM_REM
> > Time period: 2007-04-27 12:59:07 -- 2007-11-13 14:42:59
> > Total file size: 391.64MB
> > RAM: 0.02MB
>
> > I have traced all the steps that I run from the beginning , but I am
> > not sure where I am going wrong. I have copied my script below for
> > reference. This script runs for one chipType for eg.(50K_Hind240) and
> > I plan to run these steps again for the second chipType: 50K_Xba240.
>
> > library(aroma.affymetrix)
>
> > log <- Arguments$getVerbose(-8)
> > timestampOn(verbose)
>
> > dataSetName <- "katia-TumorNormal1"
> > chipTypes <- c("Mapping50K_Hind240", "Mapping50K_Xba240")
>
> > pairs <- matrix(c(
> > "TLL_ALL_10SA_REM","TLL_ALL_10SA",
> > "TLL_ALL_13BP_REM","TLL_ALL_13BP",
> > "TLL_ALL_1BD_REM","TLL_ALL_1BD",
> > "TLL_ALL_2NP_REM","TLL_ALL_2NP",
> > "TLL_ALL_3MM_REM","TLL_ALL_3MM",
> > "TLL_ALL_5NL_REM","TLL_ALL_5NL",
> > "TLL_ALL_6TA_REM","TLL_ALL_6TA",
> > "TLL_ALL_9AM_REM","TLL_ALL_9AM"
> > ),ncol=2,byrow=TRUE)
> > colnames(pairs) <- c("normal", "tumor")
>
> > chipType <- chipTypes[1]
>
> > #processing samples:
>
> > csRawList <- list()
> > for(chipType in chipTypes){
> > cs <- AffymetrixCelSet
> > $fromName(dataSetName,checkChipType=FALSE,chipType=chipType)
> > stopifnot(all(getNames(cs) %in% pairs))
> > csRawList[[chipType]]<- cs
> > }
> > print(csRawList)
>
> > #Allellic calibration
> > csAccList <- list();
> > for(chiptype in chipTypes){
> > cs <- csRawList[[chipType]]
> > acc <- AllelicCrosstalkCalibration(cs)
> > print(acc)
> > csAcc<- process(acc, verbose=log)
> > csAccList[[chipType]]<- csAcc
> > }
>
> > #Summarization
>
> > cesList<- list()
> > for(chipType in chipTypes){
> > cs <- csAccList[[chipType]]
> > plm <- RmaCnPlm(cs, mergeStrands=TRUE, combineAlleles=TRUE, E,shift=
> > +300)
> > plm
> > fit(plm, verbose=log)
> > ces <- getChipEffectSet(plm)
> > cesList[[chipType]]<- ces
> > }
>
> > #PCR fragment length normalization
> > cesFlnList<- list()
> > for(chipType in names(cesList)){
> > ces <- cesList[[chipType]]
> > fln <- FragmentLengthNormalization(ces)
> > print(fln)
> > cesFln<- process(fln,verbose=log)
> > cesFlnList[[chiptype]]<- cesFln
> > }
>
> > thanks
> > Manisha
>
> > On Oct 22, 1:13 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote:
> >> [I took the freedom to bring this thread back to the mailing list, cf
> >> FAQ. 2008-03-26]
>
> >> Hi.
>
> >> On Wed, Oct 22, 2008 at 7:17 AM,biobeewrote:
> >> > Hi Henrik,
>
> >> > Please see the details you required for troubleshooting this problem:
>
> >> > verbose output of the error:
>
> >> >> #Summarization
>
> >> >> cesList<- list()
> >> >> for(chipType in chipTypes){
> >> > + cs <- csAccList[[chipType]]
> >> > + plm <- RmaCnPlm(cs, combineAlleles=TRUE, mergeStrands=TRUE,shift=
> >> > +300)
> >> > + plm
> >> > + fit(plm, verbose=verbose)
> >> > + ces <- getChipEffectSet(plm)
> >> > + cesList[[getInputChipType]]<- ces
> >> > + }
> >> > Error in UseMethod("getCdf") : no applicable method for "getCdf"
> >> > Calls: fit -> fit.ProbeLevelModel -> getCdf
> >> > Execution halted
>
> >> > traceback() report:
> >> >> traceback()
> >> > 3: getCdf(cs)
> >> > 2: fit.ProbeLevelModel(plm, verbose = verbose)
> >> > 1: fit(plm, verbose = verbose)
>
> >> So I strongly suspect that the data set 'cs' you pass to RmaCnPlm() is
> >> NULL. For 'cs' to become NULL, the expression csAccList[[chipType]]
> >> must return NULL. Check you 'csAccList' and see if it is an empty
> >> list. Other things that come into play is the value of 'chipTypes'.
> >> You probably made a mistake earlier than what you "script" shows.
> >> This is why I keep asking everyone to post the complete script along
> >> with problem reports, because it is much easier to troubleshoot when
> >> you have the full picture.
>
> >> Cheers
>
> >> Henrik
>
> >> > sessionInfo()
> >> >> sessionInfo()
> >> > R version 2.7.2 (2008-08-25)
> >> > x86_64-unknown-linux-gnu
>
> >> > locale:
> >> > LC_CTYPE=en_US.iso885915;LC_NUMERIC=C;LC_TIME=en_US.iso885915;LC_COLLATE=en_US.iso885915;LC_MONETARY=C;LC_MESSAGES=en_US.iso885915;LC_PAPER=en_US.iso885915;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.iso885915;LC_IDENTIFICATION=C
>
> >> > attached base packages:
> >> > [1] stats graphics grDevices utils datasets methods
> >> > base
>
> >> > other attached packages:
> >> > [1] aroma.affymetrix_0.9.4 aroma.apd_0.1.3
> >> > R.huge_0.1.6
> >> > [4] affxparser_1.12.2 aroma.core_0.9.4
> >> > sfit_0.1.5
> >> > [7] aroma.light_1.8.1 digest_0.3.1
> >> > matrixStats_0.1.3
> >> > [10] R.rsp_0.3.4 R.cache_0.1.7
> >> > R.utils_1.0.4
> >> > [13] R.oo_1.4.6 R.methodsS3_1.0.3
>
> >> > Hope this helps to troubleshoot the problem.
>
> >> > thanks
> >> > manisha
>
> >> > On Jul 3, 4:14 am, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote:
> >> >> Hi,
>
> >> >> what does the verbose output show? When you get theerror, what does
> >> >> traceback() report?
>
> >> >> Also, please report your sessionInfo().
>
> >> >> /Henrik
>
> >> >> On Thu, Jun 19, 2008 at 2:09 PM,biobee<[EMAIL PROTECTED]> wrote:
>
> >> >> > I am running paired analysis on 100K samples on R 2.7.0. I get an
> >> >> >errorwhen i run the following code part:
>
> >> >> >> cesList<- list()
> >> >> >> for(chipType in chipTypes){
> >> >> > + cs <- csAccList[[chipType]]
> >> >> > + plm <- RmaCnPlm(cs, combineAlleles=TRUE, mergeStrands=TRUE,shift=
> >> >> > +300)
> >> >> > + #print(plm)
> >> >> > + fit(plm, verbose=verbose)
> >> >> > + ces <- getChipEffectSet(plm)
> >> >> > + cesList[[chipType]]<- ces
> >> >> > + }
> >> >> >ErrorinUseMethod("getCdf") :noapplicablemethodfor "getCdf"
>
> >> >> > Any suggestion will be very much appreciated.
>
> >> >> > thanks
> >> >> > manisha- Hide quoted text -
>
> >> >> - Show quoted text -- Hide quoted text -
>
> >> - Show quoted text -- Hide quoted text -
>
> >> - Show quoted text -- Hide quoted text -
>
> - Show quoted text -
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