[BioC] CGHregions error

[Daniel Rico]

Dear list, dear CGHcall developers,

I am trying to run CGHregions function (from CGHregions) package with 
copy number data from 1M arrays.

As 1 million probes are a lot, I decided to run CGHregions chromosome by 
chromosome. I am using a data.frame as input data, with copy numbers -1 
(loss), 0 (normal), +1 (gain) and +2 (amplification) as encoded in 
CGHcall package (I actually used an older version of CGHcall, that 
generated this data.frame, instead of the new cghCall object).

The funny thing is I could run it succesfully for 20 chromosomes out of 
22, but for two I'm having the following error:

Error in apply(selnew, 1, CGHregions:::.regionact2, ctdat = countsdel) :
  dim(X) must have a positive length

I have checked all the 22 data.frames and they have the same format, so 
I'm totally lost about what is going wrong with these two.

Here is an example that did not worked:

 > library(CGHregions)
 > Chr_12 <- AllCalls[AllCalls$Chr ==12 ,] # I just take probes from 
chromosome 12
 > summary(Chr_12)
          ID             Chr           Position           sample1
 cnv2414p1 :    1   12     :51627   Min.   :    21054   Min.   :-1.0000
 cnv2415p4 :    1   1      :    0   1st Qu.: 30007046   1st Qu.: 0.0000
 cnv2417p10:    1   2      :    0   Median : 65974680   Median : 0.0000
 cnv2417p19:    1   3      :    0   Mean   : 66609775   Mean   :-0.1555
 cnv2417p2 :    1   4      :    0   3rd Qu.:103296837   3rd Qu.: 0.0000
 cnv2418p2 :    1   5      :    0   Max.   :132288869   Max.   : 2.0000
 (Other)   :51621   (Other):    0
   sample2             sample3        sample4            sample5
 Min.   :-1.0000   Min.   :-1.0000   Min.   :-1.0000   Min.   :-1.000
 1st Qu.:-1.0000   1st Qu.:-1.0000   1st Qu.:-1.0000   1st Qu.: 0.000
 Median :-1.0000   Median : 0.0000   Median : 0.0000   Median : 1.000
 Mean   :-0.5257   Mean   :-0.1208   Mean   :-0.4682   Mean   : 0.608
 3rd Qu.: 0.0000   3rd Qu.: 0.0000   3rd Qu.: 0.0000   3rd Qu.: 1.000
 Max.   : 1.0000   Max.   : 2.0000   Max.   : 2.0000   Max.   : 2.000

... (55 samples in total)

 > Reg_12 <- CGHregions(Chr_12, 0.05)
[1]  5.00000000  0.02313844 18.00000000
[1] 8.00000000 0.02524250 9.00000000
[1] 11.0000000  0.0246771  7.0000000
[1] 14.0000000  0.0246771  6.0000000
[1] "Tuning on small data set finished...started with entire data set"
[1] 14.00000000  0.02602603 62.00000000  0.00000000
[1] 15.00000000  0.02285264 52.00000000
[1] 16.00000000  0.02652653 39.00000000
[1] 17.00000000  0.03439153 31.00000000
[1] 18.00000000  0.03490028 28.00000000
[1] 19.00000000  0.03703704 23.00000000
[1] 20.00000000  0.03703704 23.00000000
[1] 21.00000000  0.03240741 14.00000000
[1] 22.00000000  0.03240741 14.00000000
[1] 23.00000000  0.03703704 12.00000000
[1] 24.00000000  0.03703704 11.00000000
[1] 25.00000000  0.03703704 11.00000000
[1] 26.00000000  0.03703704 11.00000000
[1] 27.00000000  0.03703704 11.00000000
[1] 28.00000000  0.03703704 11.00000000
[1] 29.00000000  0.03703704 11.00000000
[1] 30.00000000  0.03703704 11.00000000
[1] 31.00000000  0.03703704 11.00000000
[1] 32.00000000  0.03703704 11.00000000
[1] 33.00000000  0.03703704 11.00000000
Error in apply(selnew, 1, CGHregions:::.regionact2, ctdat = countsdel) :
  dim(X) must have a positive length


 > sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-pc-linux-gnu

locale:
C

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

other attached packages:
[1] CGHregions_1.2.0 CGHbase_1.2.0    marray_1.22.0    limma_2.18.2
[5] Biobase_2.4.1

loaded via a namespace (and not attached):
[1] tools_2.9.0



Thanks for any help,
Daniel

-- 
********************************************

Daniel Rico Rodriguez, PhD.
Structural Computational Biology Group
& Bioinformatics Unit
Spanish National Cancer Research Center, CNIO
Melchor Fernandez Almagro, 3. 
28029 Madrid, Spain.
Phone: +34 91 224 69 00 #3015
drico at cnio.es
http://www.cnio.es

********************************************


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