Question: CGHregions error
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gravatar for Daniel Rico
10.0 years ago by
Daniel Rico110
Daniel Rico110 wrote:
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 ******************************************** **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y ...{{dropped:3}}
cancer cghcall cghregions • 716 views
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