[aroma.affymetrix] Error: object 'csC' not found.

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[aroma.affymetrix] Error: object 'csC' not found.

wxpyzr
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Re: [aroma.affymetrix] Error: object 'csC' not found.

Henrik Bengtsson-2
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Re: [aroma.affymetrix] Error: object 'csC' not found.

Wulc
Dear professor Henrik Bengtsson

Many thanks for your replay.

Actually, when I  created the object csC with the following code:

csC <- process(acc, verbose=verbose)

I encountered the Error: length(uPos) > 0 is not TRUE;

That's why the object 'csC' not found.

######################################

the following are the output content
> csC <- process(acc, verbose=verbose)
20160118 00:37:14|Calibrating data set for allelic cross talk...
20160118 00:37:16| Compressing model parameter to a short format...
20160118 00:37:16| Compressing model parameter to a short format...done
20160118 00:37:16| Calibrating 6 arrays...
20160118 00:37:16|  Path: probeData/cnv,ACC,ra,-XY/CytoScanHD_Array
20160118 00:37:16|  Array #1 ('01') of 6...
20160118 00:37:16|   Identifying sets of pairs of cell indices...
20160118 00:37:16|    Chip type: CytoScanHD_Array
20160118 00:37:17|    Merge shifts: TRUE
20160118 00:37:17|    Number of nucleotides: 1
20160118 00:37:17|    Locating AromaCellSequenceFile...
20160118 00:37:17|     Chip type: CytoScanHD_Array
20160118 00:37:17|     Number of cells: 6892960
     AromaCellSequenceFile:
     Name: CytoScanHD_Array
     Tags:
     Full name: CytoScanHD_Array
     Pathname: annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array.acs
     File size: 170.92 MiB (179217487 bytes)
     RAM: 0.00 MB
     Number of data rows: 6892960
     File format: v1
     Dimensions: 6892960x26
     Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
     Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
     Footer: <createdOn>20111108 21:44:22 PST</createdOn><platform>Affymetrix</platform><chipType>CytoScanHD_Array</chipType><srcFile><filename>CytoScanHD_Array.probe_tab</filename><filesize>409176930</filesize><checksum>beaaa56413608b3f9d9d464a07cddcae</checksum></srcFile><createdBy><fullname>Henrik Bengtsson</fullname>[hidden email]</createdBy>
     Chip type: CytoScanHD_Array
     Platform: Affymetrix
20160118 00:37:17|    Locating AromaCellSequenceFile...done
20160118 00:37:17|    Identifying cell indices for all non-SNP units...
20160118 00:37:17|     Non-SNP units:...
       int [1:2020614] 1 2 3 4 5 6 7 8 9 10 ...
20160118 00:37:17|      getCellIndices.AffymetrixCdfFile(): Returning cached data
20160118 00:37:17|      Non-SNP cells:...
        int [1:2037534] 6344052 5132417 3744071 1409905 879528 5837958 5341975 4106306 1391737 1201593 ...
20160118 00:37:17|      Non-SNP cells:...done
20160118 00:37:17|      Identifying the probe pairs...
20160118 00:37:17|       Units:
        NULL
20160118 00:37:17|       Checking for cached results...
20160118 00:37:17|        Found cached results
20160118 00:37:17|       Checking for cached results...done
20160118 00:37:17|      Identifying the probe pairs...done
20160118 00:37:17|      Probe shifts:
      [1] 0
20160118 00:37:17|      Identifying groups of SNP nucleotide sequence pairs...
20160118 00:37:17|       Checking for cached results...
20160118 00:37:17|       Checking for cached results...done
20160118 00:37:17|       Get SNP nucleotide sequence pairs...
20160118 00:37:17|        Retrieving SNP nucleotides...
20160118 00:37:17|         Probe shifts:
          int 0
20160118 00:37:17|         Argument 'cells':
          int [1:2, 1:2410205] 702209 3820208 6174755 2915229 1437029 2981430 4652935 141307 3892235 1614497 ...
          - attr(*, "dimnames")=List of 2
           ..$ : chr [1:2] "A" "B"
           ..$ : NULL
20160118 00:37:17|         Number of pairs: 2410205
20160118 00:37:17|         Identifying SNP positions of cell allele pairs...
20160118 00:37:17|          Checking for cached results...
20160118 00:37:18|           Found cached results
20160118 00:37:18|          Checking for cached results...done
20160118 00:37:18|         Identifying SNP positions of cell allele pairs...done
20160118 00:37:18|         SNP positions:
          int [1:2410205] NA NA NA NA NA NA NA NA NA NA ...
20160118 00:37:18|         Tabulated SNP positions:
         < table of extent 0 >
20160118 00:37:18|         Unique SNP positions:
         integer(0)
Error: length(uPos) > 0 is not TRUE
20160118 00:37:18|        Retrieving SNP nucleotides...done
20160118 00:37:18|       Get SNP nucleotide sequence pairs...done
20160118 00:37:18|      Identifying groups of SNP nucleotide sequence pairs...done
20160118 00:37:18|     Non-SNP units:...done
20160118 00:37:18|    Identifying cell indices for all non-SNP units...done
20160118 00:37:18|   Identifying sets of pairs of cell indices...done
20160118 00:37:18|  Array #1 ('01') of 6...done
20160118 00:37:18| Calibrating 6 arrays...done
20160118 00:37:18|Calibrating data set for allelic cross talk...done
> csC
Error: object 'csC' not found

#########################

the annotation file was down load from
 
http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/

However I can't solve this problem.

Could you point out what's the real problem?

Thank you very much!



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Re: [aroma.affymetrix] Error: object 'csC' not found.

ali jan
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Re: [aroma.affymetrix] Error: object 'csC' not found.

321bixin
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Re: [aroma.affymetrix] Error: object 'csC' not found.

Henrik Bengtsson-2
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Re: [aroma.affymetrix] Error: object 'csC' not found.

321bixin
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Re: [aroma.affymetrix] Error: object 'csC' not found.

Henrik Bengtsson-2
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