dear Ben
Do have plan to implement the
possibility of using RMA express in order to
normalize tilling arrays, the CEL file do have
the same format, but the CDF file does not exist
any more it is now the bpmap file ( PRNFGMm1b520182FR(-).bpmap)
i.e :
PMX PMY MMX MMY Seq Pos Probe 78 187 78 188 r2_Tag 0 TGTGATAATTTCGACGAGGCGTTAC 226 29 226 30 r2_Tag 0 CAATGATAGGCTAGTCTCGCGCAGT 257 251 257 252 r2_Tag 0 GATAAGCGTTCACAGCTCGGCAATA 174 1 174 2 r2_Tag 1 CATCCGATTAAATACCGTGGATTAC 281 107 281 108 r2_Tag 1 TAGTGCATCCTCGTGGCATCATGCG 163 102 163 103 r2_Tag 1 TGTAACGCCTCGTCGAAATTATCAC 76 61 76 62 r2_Tag 2 GCGGTCACTCAGCATATAGTCGTTG 26 41 26 42 r2_Tag 5 GCGTTACGTGAGTCTGATAGCAGTT 41 87 41 88 r2_Tag 5 CTAGCCTGCCGGTCAATAACTGATG 53 1 53 2 r2_Tag 5 ATCGTAACTCGGGTGACCAATGACC 101 29 101 30 r2_Tag 5 TGTCATGATCGTGAGTTGTCGCAGT 124 3 124 4 r2_Tag 5 TCGTTAGCCCGAGCTTAACTATTAG 314 123 314 124 r2_Tag 5 GCGTAGGTATCGACTCTCACTGTGG 164 102 164 103 r2_Tag 9 TCAGAATATGTAACGCCTCGTCGAA 171 114 171 115 r2_Tag 21 CTATTGGCTGAACTACCATGTACTG 229 171 229 172 r2_Tag 26 CATGGTAGTTCAGCCAATAGATGCC . . . 143 289 143 290 chr3 3756721 TCTCTTCCTGTACCTGAACTATGTA 37 229 37 230 chr3 3756750 GCAGAAGCCTGCAACTTCTCAATCA 36 131 36 132 chr3 3756775 CAAGCTGAGTTAAGAGCGAATACGC 245 101 245 102 chr3 3756802 AAAGCTACTCTTGTTCACGCAGCAG 314 265 314 266 chr3 3756827 CGATGCCTTCTCTTCCTGTACCTGA 164 299 164 300 chr3 3756853 CATTACAGTCTACAGAAGCCTTCAA 149 243 149 244 chr3 3756883 CAATCACAAGCTGAGTTAAGAGCGA 1 187 1 188 chr3 3756909 GACGCGCAAAGCTACTCTTGTTCAC 225 81 225 82 chr3 3756934 GCAGCAGCGATACCTTCTCTTCCTG 135 95 135 96 chr3 3756960 ACCTGAACATTACAGTCTACTCAAG 114 119 114 120 chr3 3756988 TCAACTTCTCAATCACAAGCTGAGG 259 189 259 190 chr3 3757016 GAACGTTGACACACAAAGCTACCCA 130 37 130 38 chr3 3757042 GTTCACACAGCGATGCCTTCCCTTT 122 105 122 106 chr3 3757068 TGTAACTGAACATTGCACTTTGCAG 209 323 209 324 chr3 3757092 GAAGCCTGCAACTTCTCAATCGCAA 18 125 18 126 chr3 3757120 GAAACTAGTCGTGTTCAAACTGTGG 44 197 44 198 chr3 3757146 ACCTGAGGCCTGTCCTGATTTCACC 16 273 16 274 chr3 3757171 TCAGTAGACAAACCGGAGATAGTTA 304 307 304 308 chr3 3757197 GAGTCGCAGTCTCACAACCAGGAAA 303 141 303 142 chr3 3757222 GCTCCAGCACCAAAGAGATCACTGC 322 305 322 306 chr3 3757246 CAAGAAAGTAGGAAGAATCAGGATA 116 243 116 244 chr3 3757267 GATAGAAGAGTGGAGATCCACAGGA 250 15 250 16 chr3 3757294 CGTGCGGGTCACAAGCCCATAAGGT 328 43 328 44 chr3 3757320 TCCAAGAGTGATGTGTAGCTCTGTT 12 73 12 74 chr3 3757347 TATGGATAATGAGAAGCTGAGAGTG 245 315 245 316 chr3 3757373 TGAATCTGGAGAAGAAGGTTGAGAA 93 171 93 172 chr3 3757403 GAGGGTTGAACGAATGGGTTGGATC 28 67 28 68 chr3 3757426 TCTATAGGATTAGGGAGAGAGTTTG 278 87 278 88 chr3 3757452 GAGGATGTTGAGAGGACAGAGGATG 261 223 261 224 chr3 3757479 TAAGTTTCAGATGGCGAATTTGACA 25 113 25 114 chr3 3757502 CAATGGAGAAGCTTAAGCAGATGGG 322 325 322 326 chr3 3757528 GCTTTAGCCGTTGGGCCAAGAAGAA 128 161 128 162 chr3 3757554 GCTTATACATGCAATAGGTTGTGTC 229 45 229 46 chr3 3757579 TATCACCCACATTGTCTACGTGCTT 131 79 131 80 chr3 3757600 GCTTCCTTTAACTGAGAACTATCTG 313
Hi Jun,
There are two separate issues going on here. The first is a problem with the RMAExpress code which I will go about fixing immediately. Basically what is happening is that it is detecting an error with the CEL file, but failing to properly close a modal dialog box and reactivate the main memus so it locks up.
The second issue here is actually the underlying cause of the problem. Specifically, some of the arrays are HG_U95A and some are HG_U95Av2. RMAExpress tries to ensure that all CEL files being read in are from the same array type and in this case it is finding a mismatch. In particular these are the array types for that set of files.
GSM60097.CEL: HG_U95Av2 GSM60098.CEL: HG_U95Av2 GSM60099.CEL: HG_U95A GSM60100.CEL: HG_U95A GSM60101.CEL: HG_U95A GSM60102.CEL: HG_U95A GSM60103.CEL: HG_U95A GSM60104.CEL: HG_U95A GSM60105.CEL: HG_U95A GSM60106.CEL: HG_U95A GSM60107.CEL: HG_U95A
Now this is really a special case because the U95A and U95Av2 differ based upon only a relative handful of probesets. There are several ways to handle this. The best way is to use the RMADataConv program basically following the instructions in the user guide in the subsection "Merging MG U74A and MG U74Av2 datasets" except substituting HG_U95A and HG_U95Av2 in place for the mouse array names. With the requisite file of overlap names available at:
http://bmbolstad.com/misc/mixtureCDF/HGU95Aoverlap.txt
The second way to handle this (and not necessarily recommended) is to manually edit the part of the CEL files which describes the name of appropriate array type so that they are all identical and just pretend that all the arrays are really of one type only.
Hope this helps,
Ben
On Thu, 2006-08-31 at 16:36 -0400, Jun Ding wrote: > Hi RMAExpress Developers and Users, > > I have difficulties in reading the .CEL files into RMAExpress. All the > .CEL (11) files are downloaded (GEO dataset GSE2737) and extracted, but > I can only read in the first two .CEL files. When I tried to read in > more (or only read one of the other files), RMAExpress just crashed. I > have tried RMAExpress release 0.4.1 and 0.4 alpha 7. I also got an > error message from Visual Studio Just-In-Time Debugger: "An unhandled > win32 exception occurred in RMAExpress.exe [3352]." > > Does that mean all but 2 .CEL files are corrupted? Can anyone give me > some suggestions? Thank you very much! > > Best, > Jun > > ---------------------------- > Jun Ding, Ph.D. student > Department of Biostatistics > University of Michigan > Ann Arbor, MI, 48105 > ---------------------------- > > > > > -- Ben Bolstad <bmb@xxxxxxxxxxxxx> http://bmbolstad.com
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