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
>
--
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