Dear Henrik,
Thank you very much for your help.
I compared your output with mine line by line and found no differences
until the acc command:
library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
cdf <- AffymetrixCdfFile$byChipType("Mapping250K_Nsp")
print(getChecksum(cdf))
## [1] "59ae263311a2cf63b8d1b9b4cc7d663b"
acs <- getAromaCellSequenceFile(cdf)
print(getChecksum(acs))
## [1] "b2eee634d101e645cdf616aaf1eb15f7"
ugp <- getAromaUgpFile(cdf)
print(getChecksum(ugp))
## [1] "aecffa9648f9f4fdebecf2050d9c304a"
csR <- AffymetrixCelSet$byName("GSE51265", cdf=cdf)
csR <- extract(csR, "GSM1241436")
cf <- getFile(csR, 1)
print(getChecksum(cf))
## [1] "beff390913b79fa4b7cd298125aa66a4"
acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
print(acc)
## AllelicCrosstalkCalibration:
## Data set: GSE51265
## Input tags:
## User tags: *
## Asterisk ('*') tags: ACC,-XY
## Output tags: ACC,-XY
## Number of files: 1 (62.64MB)
## Platform: Affymetrix
## Chip type: Mapping250K_Nsp
## Algorithm parameters: {rescaleBy: chr "groups", targetAvg: num [1:2]
2200 2200, subsetToAvg: int [1:6409592] 1 2 3 4 5 6 7 8 9 10 ...,
mergeShifts: logi TRUE, B: int 1, flavor: chr "sfit",
algorithmParameters:List ## of 3, ..$ 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/GSE51265,ACC,-XY/Mapping250K_Nsp
## Is done: FALSE
## RAM: 24.46MB
Eyerything seems to be identical till this point. (I also compared all the
respective outputs given by print(), which I did not copy into this
message.)
csC <- process(acc, verbose=verbose)
csC <- process(acc, verbose=verbose)
20140105 18:45:03|Calibrating data set for allelic cross talk...
20140105 18:45:03| Compressing model parameter to a short format...
20140105 18:45:03| Compressing model parameter to a short format...done
20140105 18:45:03| Calibrating 1 arrays...
20140105 18:45:03| Path: probeData/GSE51265,ACC,-XY/Mapping250K_Nsp
20140105 18:45:03| Array #1 ('GSM1241436_110830-250K_scc1') of 1...
20140105 18:45:03| setsOfProbes:
List of 2
$ snps :List of 20
..$ /C : int [1, 1:2] 24476 3820242
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "\005" "C"
..$ /A : int [1, 1:2] 24460 4037826
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "\006" "A"
..$ /A : int [1, 1:2] 24442 1513644
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "\017" "A"
..$ +/G : int [1, 1:2] 24450 1047734
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "+" "G"
..$ 0/NA : int [1, 1:2] 24438 26998
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "0" "NA"
..$ A/C : int [1:129062, 1:2] 5555562 640260 6430798 890622 858750
4681948 347160 5718766 2746760 2790782 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "A" "C"
..$ A/G : int [1:519496, 1:2] 4969704 4677672 4787718 5185370
1363100 4109892 1558340 1352256 1332280 4969616 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "A" "G"
..$ A/NA : int [1:229, 1:2] 2073542 4496254 28992 1647992 3941710
23106 225802 2711838 4178658 22352 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "A" "NA"
..$ A/T : int [1:107497, 1:2] 1028670 3832004 5665036 1832744
4167500 4571986 4938090 747094 2207654 5855716 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "A" "T"
..$ C/G : int [1:156694, 1:2] 4747206 3909704 1725666 600232 416088
1138554 6393394 6389120 555046 2960654 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "C" "G"
..$ C/NA : int [1:146, 1:2] 28678 24268 5806866 803124 4519414
1299112 2694464 6005666 22942 3266450 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "C" "NA"
..$ C/T : int [1:571788, 1:2] 3789122 5491344 768382 4974648 387402
2086744 1183506 5290380 6464728 6121838 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "C" "T"
..$ C/~ : int [1, 1:2] 2587672 24444
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "C" "~"
..$ G/NA : int [1:148, 1:2] 30118 29802 3419652 29832 22582 30846
1242456 5044168 22284 30626 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "G" "NA"
..$ G/T : int [1:124734, 1:2] 2968724 1545656 2540860 5758784
3927738 3915584 4695222 2062772 6258084 4709566 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "G" "T"
..$ G/V : int [1, 1:2] 21914 24474
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "G" "V"
..$ NA/T : int [1:219, 1:2] 28052 27998 26852 28200 26312 25758
24630 25024 28262 26766 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "NA" "T"
..$ NA/U : int [1, 1:2] 26996 24436
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "NA" "U"
..$ T/� : int [1, 1:2] 3390144 24458
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "T" "\xf0"
..$ missing: int [1:1442, 1:2] 3365154 3362594 3360034 3357474 3354914
3352354 3349794 3329314 3326754 3324194 ...
$ nonSNPs: int [1:144] 3627753 3627752 4221761 4221760 3630313 3630312
4224321 4224320 6062864 6062865 ...
- attr(*, "version")= num 4
20140105 18:45:03| Reading all probe intensities...
20140105 18:45:04| Reading all probe intensities...done
20140105 18:45:04| Fitting calibration model...
20140105 18:45:04| Allele probe-pair group #1 ('/C') of 20...
20140105 18:45:04| Fitting...
[...]
Although there are no differences between our files, I get some strange
bases and thus too many groups (19 instead of 6). Further, I get the same
error described in my first post and some warnings:
Error: Cannot rescale to target average. After taking the intersect of the
subset of cells to be used, there are no cells left.
In addition: Warning messages:
1: In regexpr("${", s, fixed = TRUE) : input string 1 is invalid UTF-8
2: In regexpr("${", s, fixed = TRUE) :
input string 1 is invalid in this locale
3: In regexpr("${", s, fixed = TRUE) :
input string 1 is invalid in this locale
4: In strsplit(name, split = "") :
input string 1 is invalid in this locale
5: In regexpr("${", s, fixed = TRUE) :
input string 1 is invalid in this locale
6: In regexpr("${", s, fixed = TRUE) :
input string 1 is invalid in this locale
7: In regexpr("${", s, fixed = TRUE) :
input string 1 is invalid in this locale
8: In regexpr("${", s, fixed = TRUE) :
input string 1 is invalid in this locale
9: In regexpr("${", s, fixed = TRUE) :
input string 1 is invalid in this locale
10: In regexpr("${", s, fixed = TRUE) :
input string 1 is invalid in this locale
It seems that something goes when reading the AromaCellSequenceFile. Maybe
something is wrong with my local R setup, but I have no idea where to look
at.
I get the same error for all my Mapping250K_Nsp data sets. However, when I
process a CytoScanHD data set on the same machine (same R version and
system settings), I get the correct sets of probes and everything runs
smoothly:
20140105 18:57:17| setsOfProbes:
List of 2
$ snps :List of 7
..$ A/C : int [1:194772, 1:2] 1523851 6765935 184921 4709415
4470065 3225268 1483811 3519189 1402645 3182682 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "A" "C"
..$ A/G : int [1:800819, 1:2] 5417905 2293549 2317137 1998181
3260641 5585387 3314241 4843917 4316355 4145525 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "A" "G"
..$ A/T : int [1:147257, 1:2] 6105275 1802427 4315733 5324513
2714739 2124739 3645755 4217717 1648067 433757 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "A" "T"
..$ C/G : int [1:214487, 1:2] 1085553 3021379 4023125 196297
4891717 4117529 3445346 2697529 609435 6410157 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "C" "G"
..$ C/T : int [1:866377, 1:2] 702209 6174755 1437029 4652935
3892235 1377845 3296559 5957417 6854975 6674391 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "C" "T"
..$ G/T : int [1:186196, 1:2] 222813 5602963 6390739 4629977
5612691 6021599 1180999 2756609 2826633 4794445 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "G" "T"
..$ missing: int [1:297, 1:2] 1163270 1660652 6511664 1804808 4657150
5266872 5577306 4137094 1871558 1931344 ...
$ nonSNPs: int [1:2037534] 6344052 5132417 3744071 1409905 879528
5837958 5341975 4106306 1391737 1201593 ...
- attr(*, "version")= num 4
I am really puzzled :/
Thanks for your help.
Best,
Hans
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