[Bioc-sig-seq] using GenomicFeatures

[Jason Lu]

Hi list,

I tried to get refseq coordinates here. It has been working well but I
encountered the following error message today.

library(GenomicFeatures)
txdb <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "refGene")
Error in tableNames(ucscTableQuery(session, track = track)) :
  error in evaluating the argument 'object' in selecting a method for
function 'tableNames': Error in GRangesForGenome(range,
seqlengths(session)) :
  Chromosome(s) 249250621, 106433, 547496, 243199373, 198022430,
191154276, 590426, 189789, 191469, 180915260, 171115067, 4622290,
4795371, 4610396, 4683263, 4833398, 4611984, 4928567, 159138663,
182896, 146364022, 38914, 37175, 141213431, 90085, 169874, 187035,
36148, 135534747, 135006516, 40103, 133851895, 115169878, 107349540,
102531392, 90354753, 81195210, 1680828, 37498, 81310, 174588, 41001,
78077248, 4262, 59128983, 92689, 159169, 63025520, 48129895, 27682,
51304566, 155270560, 59373566, 166566, 186858, 164239, 137718, 172545,
172294, 172149, 161147, 179198, 161802, 155397, 186861, 180455,
179693, 211173, 15008, 128374, 129120, 19913, 43691, 27386, 40652,
45941, 40531, 34474, 41934, 45867, 39939, 33824, 41933, 42152, 43523,
43341, 39929, 36651, 38154, 36422, 39786, 38502, 16571are invalid for:
hg19


> sessionInfo()
R version 2.14.0 Under development (unstable) (2011-04-26 r55655)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] Rsamtools_1.5.38       Biostrings_2.21.6      GenomicFeatures_1.5.14
[4] GenomicRanges_1.5.17   IRanges_1.11.11

loaded via a namespace (and not attached):
 [1] BSgenome_1.21.3    Biobase_2.13.7     DBI_0.2-5          RCurl_1.6-6
 [5] RSQLite_0.9-4      XML_3.4-0          biomaRt_2.9.2      rtracklayer_1.13.7
 [9] tools_2.14.0       zlibbioc_0.1.7

Thanks for any suggestions.

Jason