Hi Gene,
did you add additional arrays to your rawData/ directory at anytime
after having ran the pipeline ones? If so, that would explain the
problem. The solution is then to delete the two plmData/
subdirectories:
plmData/gsk,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty/
plmData/gsk,ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty/
which we give you new probe-level model estimates. The thing is that
RmaCnPlm is a multi-array method, meaning that any estimates has to be
redone if you add new arrays. Since the fragment-length normalized
data depend on this too, you have to reestimate those as well. The
easiest way is to delete the corresponding plmData/ directories as
above.
Hope this helps
Henrik
PS. Technically, you've detected a bug in RmaPlm, because it fails to
detect that new arrays have been added. Instead, it quietly pass
empty allocated chip-effect estimates to FragmentLengthNormalization
who has to deal with it ...and luckily detected it.
On Tue, Aug 17, 2010 at 8:33 PM, Gene <genetas...@gmail.com> wrote:
> Thanks for the reply, Pierre. When I ran the update, I got this
> output:
>
> ------------------------------------------------------------
> - Trying to install patches
> ------------------------------------------------------------
> No patches available for aroma.core v1.7.0.
> No patches available for aroma.affymetrix v1.7.0.
> ############################################################
> # #
> # Packages installed/updated. Please restart R. #
> # #
> ############################################################
> Warning messages:
> 1: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not
> possible
> 2: In packageDescription(pkg) : no package 'DNAcopy' was found
> 3: In safeSource() : Redefining 'biocinstall'
> 4: In safeSource() : Redefining 'biocinstallPkgGroups'
> 5: In safeSource() : Redefining 'biocinstallRepos'
>
> Given the DNAcopy error, I reinstalled DNAcopy.
>
> And then this is what happens when I rerun the normalization:
>
> ds <- lapply(chipTypes, function(x) { doCRMAv2("gsk", chipType=x,
> plm="RmaCnPlm", verbose=verbose) })
>
> CRMAv2...
> CRMAv2/Setting up CEL set...
> AffymetrixCelSet:
> Name: gsk
> Tags:
> Path: rawData/gsk/Mapping250K_Sty
> Platform: Affymetrix
> Chip type: Mapping250K_Sty
> Number of arrays: 338
> Names: ea06028_0091-02a_sty250_ss247...@pcrs,
> ea06028_0091-02e_sty250_ss247...@pcrs, ...,
> ea06028_0401-12b_sty250_ss493...@pcrs
> Time period: 2006-07-11 14:07:47 -- 2007-11-28 21:32:23
> Total file size: 21182.29MB
> RAM: 0.44MB
> CRMAv2/Setting up CEL set...done
> CRMAv2...
> Arguments:
> combineAlleles: TRUE
> arrays:
> chr ""
> ram:
> Data set
> AffymetrixCelSet:
> Name: gsk
> Tags:
> Path: rawData/gsk/Mapping250K_Sty
> Platform: Affymetrix
> Chip type: Mapping250K_Sty
> Number of arrays: 338
> Names: ea06028_0091-02a_sty250_ss247...@pcrs,
> ea06028_0091-02e_sty250_ss247...@pcrs, ...,
> ea06028_0401-12b_sty250_ss493...@pcrs
> Time period: 2006-07-11 14:07:47 -- 2007-11-28 21:32:23
> Total file size: 21182.29MB
> RAM: 0.44MB
> CRMAv2/Allelic crosstalk calibration...
> AllelicCrosstalkCalibration:
> Data set: gsk
> Input tags:
> User tags: *
> Asterisk ('*') tags: ACC,-XY
> Output tags: ACC,-XY
> Number of files: 338 (21182.29MB)
> Platform: Affymetrix
> Chip type: Mapping250K_Sty
> Algorithm parameters: (rescaleBy: chr "groups", targetAvg: num
> [1:2] 2200 2200, subsetToAvg: chr "-XY", mergeShifts: logi TRUE, B:
> int , flavor: chr "sfit", algorithmParameters:List of 3, ..$ alpha:
> num [1:8] 0.1 0.075 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num
> 2, ..$ Q: num 98)
> Output path: probeData/gsk,ACC,-XY/Mapping250K_Sty
> Is done: TRUE
> RAM: 0.01MB
> Calibrating data set for allelic cross talk...
> Already calibrated
> Calibrating data set for allelic cross talk...done
> AffymetrixCelSet:
> Name: gsk
> Tags: ACC,-XY
> Path: probeData/gsk,ACC,-XY/Mapping250K_Sty
> Platform: Affymetrix
> Chip type: Mapping250K_Sty
> Number of arrays: 338
> Names: ea06028_0091-02a_sty250_ss247...@pcrs,
> ea06028_0091-02e_sty250_ss247...@pcrs, ...,
> ea06028_0401-12b_sty250_ss493...@pcrs
> Time period: 2006-07-11 14:07:47 -- 2007-11-28 21:32:23
> Total file size: 21182.29MB
> RAM: 0.44MB
> CRMAv2/Allelic crosstalk calibration...done
> used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 2694542 144.0 8276354 442.1 8276354 442.1
> Vcells 45937133 350.5 99719322 760.8 99719322 760.8
> CRMAv2/Base position normalization...
> BasePositionNormalization:
> Data set: gsk
> Input tags: ACC,-XY
> User tags: *
> Asterisk ('*') tags: BPN,-XY
> Output tags: ACC,-XY,BPN,-XY
> Number of files: 338 (21182.29MB)
> Platform: Affymetrix
> Chip type: Mapping250K_Sty
> Algorithm parameters: (unitsToFit: chr "-XY", typesToFit: chr
> "pm", unitsToUpdate: NULL, typesToUpdate: chr "pm", shift: num 0,
> target: chr "zero", model: chr "smooth.spline", df: int 5)
> Output path: probeData/gsk,ACC,-XY,BPN,-XY/Mapping250K_Sty
> Is done: TRUE
> RAM: 0.01MB
> Normalization data set for probe-sequence effects...
> Already normalized
> Normalization data set for probe-sequence effects...done
> AffymetrixCelSet:
> Name: gsk
> Tags: ACC,-XY,BPN,-XY
> Path: probeData/gsk,ACC,-XY,BPN,-XY/Mapping250K_Sty
> Platform: Affymetrix
> Chip type: Mapping250K_Sty
> Number of arrays: 338
> Names: ea06028_0091-02a_sty250_ss247...@pcrs,
> ea06028_0091-02e_sty250_ss247...@pcrs, ...,
> ea06028_0401-12b_sty250_ss493...@pcrs
> Time period: 2006-07-11 14:07:47 -- 2007-11-28 21:32:23
> Total file size: 21182.29MB
> RAM: 0.44MB
> CRMAv2/Base position normalization...done
> used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 2830422 151.2 8276354 442.1 8276354 442.1
> Vcells 46063681 351.5 99719322 760.8 99719322 760.8
> CRMAv2/Probe summarization...
> RmaCnPlm:
> Data set: gsk
> Chip type: Mapping250K_Sty
> Input tags: ACC,-XY,BPN,-XY
> Output tags: ACC,-XY,BPN,-XY,RMA,A+B
> Parameters: (probeModel: chr "pm"; shift: num 0; flavor: chr
> "affyPLM"; treatNAsAs: chr "weights"; mergeStrands: logi TRUE;
> combineAlleles: logi TRUE).
> Path: plmData/gsk,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty
> RAM: 0.00MB
> used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 2830422 151.2 8276354 442.1 8276354 442.1
> Vcells 46063681 351.5 99719322 760.8 99719322 760.8
> CnChipEffectSet:
> Name: gsk
> Tags: ACC,-XY,BPN,-XY,RMA,A+B
> Path: plmData/gsk,ACC,-XY,BPN,-XY,RMA,A+B/Mapping250K_Sty
> Platform: Affymetrix
> Chip type: Mapping250K_Sty,monocell
> Number of arrays: 338
> Names: ea06028_0091-02a_sty250_ss247...@pcrs,
> ea06028_0091-02e_sty250_ss247...@pcrs, ...,
> ea06028_0401-12b_sty250_ss493...@pcrs
> Time period: 2010-08-09 12:53:30 -- 2010-08-09 12:54:30
> Total file size: 2940.06MB
> RAM: 0.57MB
> Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
> combineAlleles: logi TRUE)
> CRMAv2/Probe summarization...done
> CRMAv2/PCR fragment-length normalization...
> FragmentLengthNormalization:
> Data set: gsk
> Input tags: ACC,-XY,BPN,-XY,RMA,A+B
> User tags: *
> Asterisk ('*') tags: FLN,-XY
> Output tags: ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY
> Number of files: 338 (2940.06MB)
> Platform: Affymetrix
> Chip type: Mapping250K_Sty,monocell
> Algorithm parameters: (subsetToFit: chr "-XY", onMissing: chr
> "median", .target: chr "zero", shift: num 0)
> Output path: plmData/gsk,ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY/
> Mapping250K_Sty
> Is done: FALSE
> RAM: 0.00MB
> Normalizing set for PCR fragment-length effects...
> Identifying SNP and CN units...
> types
> 2
> 238378
> subsetToUpdate:
> int [1:238378] 1 2 3 4 5 6 7 8 9 10 ...
> Identifying SNP and CN units...done
> Retrieving SNP information annotations...
> UflSnpInformation:
> Name: Mapping250K_Sty
> Tags: na30,GC20100720
> Full name: Mapping250K_Sty,na30,GC20100720
> Pathname: annotationData/chipTypes/Mapping250K_Sty/
> Mapping250K_Sty,na30,GC20100720.ufl
> File size: 465.76 kB (476940 bytes)
> RAM: 0.00 MB
> Chip type: Mapping250K_Sty
> Number of enzymes: 1
> Retrieving SNP information annotations...done
> Identifying the subset used to fit normalization function(s)...
> Identifying units that are SNP and CN probes...
> UflSnpInformation:
> Name: Mapping250K_Sty
> Tags: na30,GC20100720
> Full name: Mapping250K_Sty,na30,GC20100720
> Pathname: annotationData/chipTypes/Mapping250K_Sty/
> Mapping250K_Sty,na30,GC20100720.ufl
> File size: 465.76 kB (476940 bytes)
> RAM: 0.00 MB
> Chip type: Mapping250K_Sty
> Number of enzymes: 1
> Identifying SNPs and CN probes...
> types
> 2
> 238378
> units:
> int [1:238378] 1 2 3 4 5 6 7 8 9 10 ...
> Identifying SNPs and CN probes...done
> Identify subset of units from genome information...
> subsetToFit: -XY
> UgpGenomeInformation:
> Name: Mapping250K_Sty
> Tags: na30,GC20100720
> Full name: Mapping250K_Sty,na30,GC20100720
> Pathname: annotationData/chipTypes/Mapping250K_Sty/
> Mapping250K_Sty,na30,GC20100720.ugp
> File size: 1.14 MB (1192500 bytes)
> RAM: 0.00 MB
> Chip type: Mapping250K_Sty
> Units to exclude:
> int [1:4812] 57520 57521 57524 57527 57529 57530 57531
> 57534 57536 57539 ...
> Units to include:
> int [1:233566] 1 2 3 4 5 6 7 8 9 10 ...
> Identify subset of units from genome information...done
> Reading fragment lengths...
> Reading fragment lengths...done
> Identifying units that are SNP and CN probes...done
> int [1:233566] 1 2 3 4 5 6 7 8 9 10 ...
> Identifying the subset used to fit normalization
> function(s)...done
> Shift: 0
> onMissing: median
> Array #1 of 338 ('ea06028_0091-02a_sty250_ss247...@pcrs')...
> V1
> Min. : NA
> 1st Qu.: NA
> Median : NA
> Mean : NaN
> 3rd Qu.: NA
> Max. : NA
> NA's :238378
> int [1:233566] 1 2 3 4 5 6 7 8 9 10 ...
> UflSnpInformation:
> Name: Mapping250K_Sty
> Tags: na30,GC20100720
> Full name: Mapping250K_Sty,na30,GC20100720
> Pathname: annotationData/chipTypes/Mapping250K_Sty/
> Mapping250K_Sty,na30,GC20100720.ufl
> File size: 465.76 kB (476940 bytes)
> RAM: 0.91 MB
> Chip type: Mapping250K_Sty
> Number of enzymes: 1
> Setting up predefined target functions...
> Target type: zero
> Setting up predefined target functions...done
> Getting cell matrix map...
> 'UnitGroupCellMatrixMap' int [1:238378, 1] 1 2 3 4 5 6 7 8 9
> 10 ...
> Getting cell matrix map...done
> Getting theta estimates...
> Thetas:
> num [1:238378, 1] 1009 584 1569 1216 259 ...
> num [1:238378, 1] 1009 584 1569 1216 259 ...
> V1
> Min. : 100.1
> 1st Qu.: 4651.1
> Median : 7006.5
> Mean : 8231.1
> 3rd Qu.:10648.0
> Max. :88987.9
> Getting theta estimates...done
> Calculating total signals...
> Total thetas:
> num [1:238378] 1009 584 1569 1216 259 ...
> Calculating total signals...done
> Normalizing log2 signals...
> Log2 signals:
> num [1:238378] 9.98 9.19 10.62 10.25 8.01 ...
> Error in list(`lapply(chipTypes, function(x) {` = <environment>,
> `lapply.default(chipTypes, function(x) {` = <environment>, :
>
> [2010-08-17 11:28:04] Exception: Cannot fit normalization function to
> enzyme, because there are no (finite) data points that are unique to
> this enzyme: 1
> at throw(Exception(...))
> at throw.default("Cannot fit normalization function to enzyme,
> because there a
> at throw("Cannot fit normalization function to enzyme, because there
> are no (f
> at normalizeFragmentLength.default(y, fragmentLengths = fl,
> targetFcns = targe
> at normalizeFragmentLength(y, fragmentLengths = fl, targetFcns =
> targetFcns, s
> at process.FragmentLengthNormalization(fln, verbose = verbose)
> at process(fln, verbose = verbose)
> at doCRMAv2.AffymetrixCelSet(csR, ..., verbose = verbose)
> at doCRMAv2(csR, ..., verbose = verbose)
> at doCRMAv2.character("gsk", chipType = x, plm = "RmaCnPlm", verbose
> = verbose
> at doCRMAv2("gsk", chipType = x, plm = "RmaCnPlm", verbose =
> verbose)
> at FUN(c("Mapping250K_Sty", "Mapping250K_Nsp")[[1]], ...)
> at lapply.default(chipTypes, function(x) {
> at lapply(chipTypes
> Normalizing log2 signals...done
> Array #1 of 338
> ('ea06028_0091-02a_sty250_ss247...@pcrs')...done
> Normalizing set for PCR fragment-length effects...done
>
>
> Gene
>
>
> On Aug 16, 4:44 pm, Pierre Neuvial <pie...@stat.berkeley.edu> wrote:
>
>> Can you update aroma.affymetrix to the most recent version (1.7.0):
>>
>> source("http://aroma-project.org/hbLite.R";);
>> hbInstall("aroma.affymetrix");
>>
>> and then paste the output of
>>
>> verbose <- Arguments$getVerbose(-8)
>> ds <- lapply(chipTypes, function(x) {
>> doCRMAv2("gsk", chipType=x, plm="RmaCnPlm", verbose=verbose)
>>
>> })
>>
>> ?
>>
>> Thanks,
>>
>> Pierre
>>
>
> --
> 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/
>
--
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/
