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. 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.