I am having a problem with the chromLoc object while trying to use the cset2band method in the reb package. I am trying to do a genome wide cytogenic analysis. Here is my full code. library(affy) library(hgu133plus2.db) library(hgu133plus2barcodevecs) library(hgu133plus2cdf) library(idiogram) library(reb) expr <- justRMA() matrix <- assayData(expr)$exprs #Define oncocytoma as norms norms <- 16:30 chr <- buildChromLocation.2("hgu133plus2.db","bands") cset <- reb(matrix,chr,ref=norms,center=TRUE) exprs <- cset[,-norms] exprs[abs(exprs) < 1.96] <- NA banded <- cset2band(exprs,chr,FUN=mean,na.rm=TRUE) h.cyto <- buildChromCytoband(organism = "h") midiogram(banded,h.cyto,method="i",col=.rwb,dlim=c(-4,4)) This is based off of the reference manual for the reb package. At the cset2band line, I get the following error: Error in get(chr, cytoEnv) : object '6_ssto_hap7' not found I believe this is due to the fact that my chr object contains additional chromosomes and I'm not sure how to deal with them. contents of chr: Instance of a chromLocation class with the following fields: Organism: Homo sapiens Data source: hgu133plus2.db Number of chromosomes for this organism: 93 Chromosomes of this organism and their lengths in base pairs: 1 : 249250621 2 : 243199373 3 : 198022430 4 : 191154276 5 : 180915260 6 : 171115067 7 : 159138663 X : 155270560 8 : 146364022 9 : 141213431 10 : 135534747 11 : 135006516 12 : 133851895 13 : 115169878 14 : 107349540 15 : 102531392 16 : 90354753 17 : 81195210 18 : 78077248 20 : 63025520 Y : 59373566 19 : 59128983 22 : 51304566 21 : 48129895 6_ssto_hap7 : 4928567 6_mcf_hap5 : 4833398 6_cox_hap2 : 4795371 6_mann_hap4 : 4683263 6_apd_hap1 : 4622290 6_qbl_hap6 : 4611984 6_dbb_hap3 : 4610396 17_ctg5_hap1 : 1680828 4_ctg9_hap1 : 590426 1_gl000192_random : 547496 Un_gl000225 : 211173 4_gl000194_random : 191469 4_gl000193_random : 189789 9_gl000200_random : 187035 Un_gl000222 : 186861 Un_gl000212 : 186858 7_gl000195_random : 182896 Un_gl000223 : 180455 Un_gl000224 : 179693 Un_gl000219 : 179198 17_gl000205_random : 174588 Un_gl000215 : 172545 Un_gl000216 : 172294 Un_gl000217 : 172149 9_gl000199_random : 169874 Un_gl000211 : 166566 Un_gl000213 : 164239 Un_gl000220 : 161802 Un_gl000218 : 161147 19_gl000209_random : 159169 Un_gl000221 : 155397 Un_gl000214 : 137718 Un_gl000228 : 129120 Un_gl000227 : 128374 1_gl000191_random : 106433 19_gl000208_random : 92689 9_gl000198_random : 90085 17_gl000204_random : 81310 Un_gl000233 : 45941 Un_gl000237 : 45867 Un_gl000230 : 43691 Un_gl000242 : 43523 Un_gl000243 : 43341 Un_gl000241 : 42152 Un_gl000236 : 41934 Un_gl000240 : 41933 17_gl000206_random : 41001 Un_gl000232 : 40652 Un_gl000234 : 40531 11_gl000202_random : 40103 Un_gl000238 : 39939 Un_gl000244 : 39929 Un_gl000248 : 39786 8_gl000196_random : 38914 Un_gl000249 : 38502 Un_gl000246 : 38154 17_gl000203_random : 37498 8_gl000197_random : 37175 Un_gl000245 : 36651 Un_gl000247 : 36422 9_gl000201_random : 36148 Un_gl000235 : 34474 Un_gl000239 : 33824 21_gl000210_random : 27682 Un_gl000231 : 27386 Un_gl000229 : 19913 M : 16571 Un_gl000226 : 15008 18_gl000207_random : 4262 > Thanks, Tejas =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use\...{{dropped:16}}

Thanks for the report and the example. The package maintainer is on summer holiday for the next few days so there may be a delay in his reply. I think you can manually specify the chromosome names using the "chr" argument in the cset2band() function call. The syntax will be a bit confusing because in your example "chr" is also the variable name for the chromLoc object. banded <- cset2band(exprs=exprs,genome=chr,chr=c(1:22,"X","Y"),FUN=mea n,na.rm=TRUE) This will hopefully bypass the more cryptic names in the chromLoc object and help move the process along. -kyle On 6/24/10 3:58 PM, "Sathe, Tejas" <sathet at="" ccf.org=""> wrote: I am having a problem with the chromLoc object while trying to use the cset2band method in the reb package. I am trying to do a genome wide cytogenic analysis. Here is my full code. library(affy) library(hgu133plus2.db) library(hgu133plus2barcodevecs) library(hgu133plus2cdf) library(idiogram) library(reb) expr <- justRMA() matrix <- assayData(expr)$exprs #Define oncocytoma as norms norms <- 16:30 chr <- buildChromLocation.2("hgu133plus2.db","bands") cset <- reb(matrix,chr,ref=norms,center=TRUE) exprs <- cset[,-norms] exprs[abs(exprs) < 1.96] <- NA banded <- cset2band(exprs,chr,FUN=mean,na.rm=TRUE) h.cyto <- buildChromCytoband(organism = "h") midiogram(banded,h.cyto,method="i",col=.rwb,dlim=c(-4,4)) This is based off of the reference manual for the reb package. At the cset2band line, I get the following error: Error in get(chr, cytoEnv) : object '6_ssto_hap7' not found I believe this is due to the fact that my chr object contains additional chromosomes and I'm not sure how to deal with them. contents of chr: Instance of a chromLocation class with the following fields: Organism: Homo sapiens Data source: hgu133plus2.db Number of chromosomes for this organism: 93 Chromosomes of this organism and their lengths in base pairs: 1 : 249250621 2 : 243199373 3 : 198022430 4 : 191154276 5 : 180915260 6 : 171115067 7 : 159138663 X : 155270560 8 : 146364022 9 : 141213431 10 : 135534747 11 : 135006516 12 : 133851895 13 : 115169878 14 : 107349540 15 : 102531392 16 : 90354753 17 : 81195210 18 : 78077248 20 : 63025520 Y : 59373566 19 : 59128983 22 : 51304566 21 : 48129895 6_ssto_hap7 : 4928567 6_mcf_hap5 : 4833398 6_cox_hap2 : 4795371 6_mann_hap4 : 4683263 6_apd_hap1 : 4622290 6_qbl_hap6 : 4611984 6_dbb_hap3 : 4610396 17_ctg5_hap1 : 1680828 4_ctg9_hap1 : 590426 1_gl000192_random : 547496 Un_gl000225 : 211173 4_gl000194_random : 191469 4_gl000193_random : 189789 9_gl000200_random : 187035 Un_gl000222 : 186861 Un_gl000212 : 186858 7_gl000195_random : 182896 Un_gl000223 : 180455 Un_gl000224 : 179693 Un_gl000219 : 179198 17_gl000205_random : 174588 Un_gl000215 : 172545 Un_gl000216 : 172294 Un_gl000217 : 172149 9_gl000199_random : 169874 Un_gl000211 : 166566 Un_gl000213 : 164239 Un_gl000220 : 161802 Un_gl000218 : 161147 19_gl000209_random : 159169 Un_gl000221 : 155397 Un_gl000214 : 137718 Un_gl000228 : 129120 Un_gl000227 : 128374 1_gl000191_random : 106433 19_gl000208_random : 92689 9_gl000198_random : 90085 17_gl000204_random : 81310 Un_gl000233 : 45941 Un_gl000237 : 45867 Un_gl000230 : 43691 Un_gl000242 : 43523 Un_gl000243 : 43341 Un_gl000241 : 42152 Un_gl000236 : 41934 Un_gl000240 : 41933 17_gl000206_random : 41001 Un_gl000232 : 40652 Un_gl000234 : 40531 11_gl000202_random : 40103 Un_gl000238 : 39939 Un_gl000244 : 39929 Un_gl000248 : 39786 8_gl000196_random : 38914 Un_gl000249 : 38502 Un_gl000246 : 38154 17_gl000203_random : 37498 8_gl000197_random : 37175 Un_gl000245 : 36651 Un_gl000247 : 36422 9_gl000201_random : 36148 Un_gl000235 : 34474 Un_gl000239 : 33824 21_gl000210_random : 27682 Un_gl000231 : 27386 Un_gl000229 : 19913 M : 16571 Un_gl000226 : 15008 18_gl000207_random : 4262 > Thanks, Tejas =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use\...{{dropped:19}}