Hi,
it turns out that this was fixed in aroma.light v1.30.1(*). Now,
aroma.light (>= 1.30.1) is part of Bioc v2.12 which is for R (>=
3.0.0). You are using R 2.15.1. So, in order for you do fix this
problem, you have to upgrade R. This is something you should either
way, because during the last 2 years lots of things have improved,
several bug have been fixed and so on (both in R, BioC and aroma).
Current stable release is R 3.1.0 (April 2014). Also, the next
release of aroma.affymetrix et al. will require at least R (>= 3.0.1).
(*) Details from news(package="aroma.light"):
Version: 1.30.1 [2013-04-18]:
o BUG FIX: backtransformPrincipalCurve() gave an error if the
pricipal curve was fitted using data with missing values.
Hope this helps
Henrik
On Fri, May 2, 2014 at 1:33 AM, Clara Tang <clara...@gmail.com> wrote:
> Dear Henrik,
>
> Thanks for your prompt reply. When I type sessionInfo(), the output is as
> follows,
>
>>sessionInfo()
>
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_HK.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_HK.UTF-8 LC_COLLATE=en_HK.UTF-8
> [5] LC_MONETARY=en_HK.UTF-8 LC_MESSAGES=en_HK.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_HK.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] aroma.affymetrix_2.12.0 aroma.light_1.24.0 aroma.cn_1.5.0
> [4] aroma.core_2.12.1 R.devices_2.8.2 R.filesets_2.4.0
> [7] R.utils_1.29.8 R.oo_1.18.0 affxparser_1.28.1
> [10] R.methodsS3_1.6.1
>
> loaded via a namespace (and not attached):
> [1] aroma.apd_0.5.0 base64enc_0.1-1 digest_0.6.4 DNAcopy_1.30.0
> [5] matrixStats_0.8.14 PSCBS_0.40.4 R.cache_0.9.2 R.huge_0.8.0
> [9] R.rsp_0.15.0 tools_2.15.1
>
> Is there any problem with the version of Aroma files? I just updated them
> recently but the workspace was built a while ago.
>
> Regards,
> Clara
>
>
> On Sunday, April 27, 2014 5:35:47 PM UTC+8, Clara Tang wrote:
>>
>> Hi,
>>
>> I am trying to perform cross platform normalization for CytoScan and Omni
>> using MSCN but the program stops after smoothing. I imported the Affymetrix
>> raw intensity data and called the totalCn and Baf using CRMAv2 and CalMate.
>> LogR ratio (log2 scale) and BAF were extracted using GenomeStudio for Omni
>> and imported as 2^LRR*2 and BAF into .total.asb and .fracB.asb respectively.
>> Plotting the CN indicated similar level of mean intensities for both
>> platforms (CN~1) and thereby I proceeded to perform the mscn. Smoothing
>> looks normal but after that, the program seemed to stop while
>> backtransforming.
>>
>> May I know how I can overcome the error of smooth.spline(sKK, lambda,
>> ...)?? What's wrong in my data?
>>
>> Thanks a lot!!!!!!
>>
>> --Clara
>>
>> P.S. Log file is pasted as below,
>>
>> =====================================================
>> dsNList <- process(mscn, verbose=log)
>> 20140427 17:06:46|Multi-source normalize all samples...
>> 20140427 17:06:46| Number of unique samples in all sets: 8
>> chr [1:8] "9C" "9C-2" "2C" "2C-2" "4C" ...
>> 20140427 17:06:46| Processing each array...
>> 20140427 17:06:46| Sample #1 ('9C') of 8...
>> 20140427 17:06:46| Identifying source data files...
>> 20140427 17:06:46| Getting list tuple of data files for one sample...
>> 20140427 17:06:46| Sample name: 9C
>> 20140427 17:06:47| Number of arrays: 2
>> 20140427 17:06:47| Getting list tuple of data files for one
>> sample...done
>> [[1]]
>> AromaUnitTotalCnBinaryFile:
>> Name: 9C
>> Tags: total
>> Full name: 9C,total
>> Pathname:
>> totalAndFracBData/Cytoscan,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2/CytoScanHD_Array/9C,total.asb
>> File size: 10.77 MB (11288937 bytes)
>> RAM: 0.01 MB
>> Number of data rows: 2822125
>> File format: v1
>> Dimensions: 2822125x1
>> Column classes: double
>> Number of bytes per column: 4
>> Footer: <createdOn>20140421 18:35:53
>> HKT</createdOn><platform>Affymetrix</platform><chipType>CytoScanHD_Array</chipType><srcFile><srcDataSet>Cytoscan,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY</srcDataSet><srcChipType>CytoScanHD_Array,monocell</srcChipType><srcFullName>9C,chipEffects</srcFullName><srcChecksum>7d70e31c6aa60b7d8664373333ad5452</srcChecksum></srcFile>
>> Platform: Affymetrix
>> Chip type: CytoScanHD_Array
>>
>> [[2]]
>> AromaUnitTotalCnBinaryFile:
>> Name: 9C
>> Tags:9C,ratio,total
>> Full name: 9C,9C,ratio,total
>> Pathname: totalAndFracBData/Omni/HumanOmni2.5/9C,9C,ratio,total.asb
>> File size: 9.08 MB (9519600 bytes)
>> RAM: 0.01 MB
>> Number of data rows: 2379855
>> File format: v1
>> Dimensions: 2379855x1
>> Column classes: double
>> Number of bytes per column: 4
>> Footer: <createdOn>20140427 16:14:31
>> HKT</createdOn><platform>Illumina</platform><chipType>HumanOmni2.5</chipType>
>> Platform: Illumina
>> Chip type: HumanOmni2.5
>>
>> 20140427 17:06:47| Identifying source data files...done
>> 20140427 17:06:47| Check if all arrays are already normalized...
>> 20140427 17:06:47| Is done: FALSE
>> 20140427 17:06:47| Check if all arrays are already normalized...done
>> 20140427 17:06:47| Fitting model...
>> 20140427 17:06:47| Fitting one sample across multiple sources...
>> 20140427 17:06:47| Number of arrays: 2
>> 20140427 17:06:47| Sample name: 9C
>> List of 4
>> $ subsetToFit : int [1:28781] 1 2 3 4 5 6 7 8 9 10 ...
>> $ fitUgp :Classes 'AromaUgpFile',
>> 'AromaUnitChromosomeTabularBinaryFile', 'AromaUnitTabularBinaryFile',
>> 'UnitAnnotationDataFile', 'AromaMicroarrayTabularBinaryFile',
>> 'AromaPlatformInterface', 'AromaTabularBinaryFile', 'FileCacheKeyInterface',
>> 'CacheKeyInterface', 'GenericTabularFile', 'ColumnNamesInterface',
>> 'GenericDataFile', 'FullNameInterface', 'Object' atomic [1:1] NA
>> .. ..- attr(*, ".env")=<environment: 0x3c8f518>
>> $ align : chr "byChromosome"
>> $ targetDimension: int 1
>> 20140427 17:06:47| Getting list tuple of data files for one sample...
>> 20140427 17:06:47| Sample name: 9C
>> 20140427 17:06:47| Number of arrays: 2
>> 20140427 17:06:47| Getting list tuple of data files for one
>> sample...done
>> List of 2
>> $ :Classes 'AromaUnitTotalCnBinaryFile', 'CopyNumberDataFile',
>> 'AromaUnitSignalBinaryFile', 'AromaPlatformInterface',
>> 'AromaTabularBinaryFile', 'FileCacheKeyInterface', 'CacheKeyInterface',
>> 'GenericTabularFile', 'ColumnNamesInterface', 'GenericDataFile',
>> 'FullNameInterface', 'Object' atomic [1:1] NA
>> .. ..- attr(*, ".env")=<environment: 0x67be7f0>
>> $ :Classes 'AromaUnitTotalCnBinaryFile', 'CopyNumberDataFile',
>> 'AromaUnitSignalBinaryFile', 'AromaPlatformInterface',
>> 'AromaTabularBinaryFile', 'FileCacheKeyInterface', 'CacheKeyInterface',
>> 'GenericTabularFile', 'ColumnNamesInterface', 'GenericDataFile',
>> 'FullNameInterface', 'Object' atomic [1:1] NA
>> .. ..- attr(*, ".env")=<environment: 0x36d2f48>
>> 20140427 17:06:47| Extracting data...
>> 20140427 17:06:47| Subset of units used for fitting:
>> int [1:28781] 1 2 3 4 5 6 7 8 9 10 ...
>> num [1:28781, 1:2] 0.561 0.566 0.798 0.861 0.81 ...
>> V1 V2
>> Min. :-0.7285 Min. :-1.9090
>> 1st Qu.: 0.9677 1st Qu.: 0.9403
>> Median : 0.9842 Median : 0.9838
>> Mean : 0.9805 Mean : 0.9898
>> 3rd Qu.: 0.9995 3rd Qu.: 1.0340
>> Max. : 1.3343 Max. : 1.9075
>> NA's :1865 NA's :1934
>> 20140427 17:06:48| Extracting data...done
>> 20140427 17:06:48| Fitting across-source normalization function...
>> 20140427 17:06:48| Estimator for principal curves:
>> function (Y, ...)
>> - attr(*, "smoother")=function (lambda, xj, ...)
>> - attr(*, "df")= num 5
>> 20140427 17:07:52| Fitting time:
>> user system elapsed
>> 63.884 0.008 64.062
>> 20140427 17:07:52| Direction of fitted curve ('lambda') was flipped
>> such that it increases with the signal.
>> 20140427 17:07:52| Processing time: 64.1 seconds
>> List of 7
>> $ s : num [1:28781, 1:2] 0.652 0.652 0.665 NA 0.836
>> ...
>> $ tag : num [1:28781] 15371 15372 7262 NA 15373 ...
>> $ lambda : num [1:28781] 1.99 1.99 1.93 NA 1.38 ...
>> $ dist : num 31.6
>> $ converged : logi TRUE
>> $ nbrOfIterations: int 6
>> $ call : language principal.curve(x = X, smoother = ..1,
>> trace = trace)
>> - attr(*, "class")= chr [1:2] "PrincipalCurve" "principal.curve"
>> - attr(*, "processingTime")=Class 'proc_time' Named num [1:5] 63.8
>> 0.004 63.975 0 0
>> .. ..- attr(*, "names")= chr [1:5] "user.self" "sys.self"
>> "elapsed" "user.child" ...
>> 20140427 17:07:52| Fitting across-source normalization function...done
>> 20140427 17:07:52| Calculating shift for each chromosome...
>> 20140427 17:07:52| align=byChromosome
>> 20140427 17:07:52| Chromosomes: 1-25
>> 20140427 17:07:52| Grouping units by chromosome...
>> List of 24
>> $ Chr01: int [1:2472] 1 2 3 4 5 6 7 8 9 10 ...
>> $ Chr02: int [1:2434] 2473 2474 2475 2476 2477 2478 2479 2480 2481
>> 2482 ...
>> $ Chr03: int [1:1995] 4907 4908 4909 4910 4911 4912 4913 4914 4915
>> 4916 ...
>> $ Chr04: int [1:1917] 6902 6903 6904 6905 6906 6907 6908 6909 6910
>> 6911 ...
>> $ Chr05: int [1:1810] 8819 8820 8821 8822 8823 8824 8825 8826 8827
>> 8828 ...
>> $ Chr06: int [1:1709] 10629 10630 10631 10632 10633 10634 10635
>> 10636 10637 10638 ...
>> $ Chr07: int [1:1589] 12338 12339 12340 12341 12342 12343 12344
>> 12345 12346 12347 ...
>> $ Chr08: int [1:1463] 13927 13928 13929 13930 13931 13932 13933
>> 13934 13935 13936 ...
>> $ Chr09: int [1:1405] 15390 15391 15392 15393 15394 15395 15396
>> 15397 15398 15399 ...
>> $ Chr10: int [1:1355] 16795 16796 16797 16798 16799 16800 16801
>> 16802 16803 16804 ...
>> $ Chr11: int [1:1350] 18150 18151 18152 18153 18154 18155 18156
>> 18157 18158 18159 ...
>> $ Chr12: int [1:1335] 19500 19501 19502 19503 19504 19505 19506
>> 19507 19508 19509 ...
>> $ Chr13: int [1:1142] 20835 20836 20837 20838 20839 20840 20841
>> 20842 20843 20844 ...
>> $ Chr14: int [1:1064] 21977 21978 21979 21980 21981 21982 21983
>> 21984 21985 21986 ...
>> $ Chr15: int [1:1004] 23041 23042 23043 23044 23045 23046 23047
>> 23048 23049 23050 ...
>> $ Chr16: int [1:900] 24045 24046 24047 24048 24049 24050 24051
>> 24052 24053 24054 ...
>> $ Chr17: int [1:817] 24945 24946 24947 24948 24949 24950 24951
>> 24952 24953 24954 ...
>> $ Chr18: int [1:778] 25762 25763 25764 25765 25766 25767 25768
>> 25769 25770 25771 ...
>> $ Chr19: int [1:639] 26540 26541 26542 26543 26544 26545 26546
>> 26547 26548 26549 ...
>> $ Chr20: int [1:637] 27179 27180 27181 27182 27183 27184 27185
>> 27186 27187 27188 ...
>> $ Chr21: int [1:470] 27816 27817 27818 27819 27820 27821 27822
>> 27823 27824 27825 ...
>> $ Chr22: int [1:496] 28286 28287 28288 28289 28290 28291 28292
>> 28293 28294 28295 ...
>> $ Chr23: int [1:1550] 28782 28783 28784 28785 28786 28787 28788
>> 28789 28790 28791 ...
>> $ Chr24: int [1:578] 30332 30333 30334 30335 30336 30337 30338
>> 30339 30340 30341 ...
>> 20140427 17:07:52| Grouping units by chromosome...done
>> 20140427 17:07:52| Allocating matrix for smooth data...
>> 20140427 17:07:52| RAM: 494760 bytes
>> 20140427 17:07:52| Allocating matrix for smooth data...done
>> 20140427 17:07:52| Loading and backtransforming *smoothed* data...
>> 20140427 17:07:52| Source #1 ('9C,total') of 2...
>> 20140427 17:07:52| Loading smoothed data...
>> num [1:30910] 0.561 0.566 0.798 0.861 0.81 ...
>> 20140427 17:07:52| Loading smoothed data...done
>> 20140427 17:07:52| Backtransforming smoothed data...
>> Error in smooth.spline(sKK, lambda, ...) :
>> missing or infinite values in inputs are not allowed
>> 20140427 17:07:52| Backtransforming smoothed data...done
>> 20140427 17:07:52| Source #1 ('9C,total') of 2...done
>> 20140427 17:07:52| Loading and backtransforming *smoothed*
>> data...done
>> 20140427 17:07:52| Calculating shift for each chromosome...done
>> 20140427 17:07:52| Fitting one sample across multiple sources...done
>> 20140427 17:07:52| Fitting model...done
>> 20140427 17:07:52| Sample #1 ('9C') of 8...done
>> 20140427 17:07:52| Processing each array...done
>> 20140427 17:07:52|Multi-source normalize all samples...done
>>
> --
> --
> 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/
>
> ---
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--
--
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
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