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}}

