Hi,
I haven't seen this before, but it certainly looks like something went
wrong when aroma tried to infer the SNP nucleotide pairs for that chip
type. This can either be due to issues reading the CDF or the ACS
file. Before continuing, check one more time that your CDF and ACS
files have identical checksums as mine. Then, lets start by clearing
the file cache:
# Clear cache
> library("R.cache")
> clearCache(dirs="aroma.affymetrix", recursive=TRUE, prompt=FALSE)
# Make sure cache is empty
> dir(getCachePath(dirs="aroma.affymetrix"))
character(0)
Now, restart R and try with aroma again. If that works, there must
have been a hiccup in the spacetime at some point. Let me know.
/Henrik
On Sun, Jan 5, 2014 at 10:02 AM, Hans-Ulrich
<hans-ulrich.kl...@uni-muenster.de> wrote:
> 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
>
> --
> --
> 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.
>
>
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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
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