[Bioc-devel] hgu95aprobe missing sequences

[Ernest Turro]

Dear Biocore Data Team,

The hgu95aprobe package appears to be missing sequence information  
for 172 transcripts, yet this information is available on the  
Affymetrix web site:

 > seqs <- read.delim("HG_U95A_probe_tab") # http:// 
www.affymetrix.com/analysis/downloads/data/HG-U95A_probe_tab.zip
 > nrow(seqs)
[1] 201807

 > d <- ReadAffy("1521a99hpp_av06.CEL") # http://www.affymetrix.com/ 
analysis/downloads/data/1521ak.zip
 > length(pm(d))
[1] 201807

 > length(hgu95aprobe$seq) # should be 201807
[1] 199091

 > geneNames(d)[!geneNames(d) %in% hgu95aprobe$Probe.Set.Name]
   [1] "1142_at"   "1143_s_at" "1144_at"   "1145_g_at" "1146_at"    
"1147_at"
   [7] "1148_s_at" "1149_at"   "1150_at"   "1151_at"   "1162_g_at"  
"1163_at"
  [13] "1164_at"   "1170_at"   "1171_s_at" "1172_at"   "1173_g_at"  
"1174_at"
  [19] "1175_s_at" "1176_at"   "1177_at"   "1178_at"   "1179_at"    
"1180_g_at"
  [25] "1181_at"   "1278_at"   "1279_s_at" "1280_i_at" "1281_f_at"  
"1282_s_at"
  [31] "1283_at"   "1284_at"   "1285_at"   "1286_s_at" "1428_at"    
"1513_at"
  [37] "1514_g_at" "1515_at"   "1516_g_at" "1608_at"   "1609_g_at"  
"1623_s_at"
  [43] "1624_at"   "1625_at"   "1626_at"   "1627_at"   "1628_at"    
"1629_s_at"
  [49] "1630_s_at" "1631_at"   "1632_at"   "1661_i_at" "1662_r_at"  
"1663_at"
  [55] "1664_at"   "1665_s_at" "1725_s_at" "1726_at"   "1743_s_at"  
"1744_at"
  [61] "1745_at"   "1746_s_at" "1790_s_at" "1812_s_at" "1813_at"    
"1818_at"
  [67] "1819_at"   "1820_g_at" "1821_at"   "1822_at"   "1823_g_at"  
"1837_at"
  [73] "1838_g_at" "1839_at"   "1840_g_at" "1841_s_at" "1842_at"    
"1843_at"
  [79] "1876_at"   "1877_g_at" "1881_at"   "1882_g_at" "1883_s_at"  
"1892_s_at"
  [85] "1893_s_at" "1894_f_at" "1903_at"   "1905_s_at" "1906_at"    
"1921_at"
  [91] "1922_g_at" "1936_s_at" "1937_at"   "292_s_at"  "293_at"     
"294_s_at"
  [97] "295_s_at"  "296_at"    "297_g_at"  "298_at"    "299_i_at"   
"300_f_at"
[103] "301_at"    "302_at"    "303_at"    "304_at"    "305_g_at"   
"311_s_at"
[109] "312_s_at"  "313_at"    "323_at"    "324_f_at"  "325_s_at"   
"326_i_at"
[115] "327_f_at"  "328_at"    "329_s_at"  "330_s_at"  "331_at"     
"332_at"
[121] "333_s_at"  "334_s_at"  "335_r_at"  "693_g_at"  "694_at"     
"695_at"
[127] "696_at"    "697_f_at"  "698_f_at"  "699_s_at"  "700_s_at"   
"701_s_at"
[133] "702_f_at"  "703_at"    "704_at"    "705_at"    "706_at"     
"707_s_at"
[139] "711_at"    "712_s_at"  "713_at"    "714_at"    "723_s_at"   
"724_at"
[145] "725_i_at"  "726_f_at"  "727_at"    "728_at"    "729_i_at"   
"730_r_at"
[151] "731_f_at"  "732_f_at"  "733_at"    "734_at"    "735_s_at"   
"918_at"
[157] "919_at"    "920_at"    "921_s_at"  "936_s_at"  "937_at"     
"938_at"
[163] "939_at"    "952_at"    "953_g_at"  "954_s_at"  "955_at"     
"956_at"
[169] "957_at"    "958_s_at"  "959_at"    "960_g_at"


Best,

Ernest Turro