Copy number Variation analysis using conumee

Question

[gs000095]

Dear All, I want to perform copy number variation analysis using conumee package in R. After going through its vignette, I loaded in my combined array data,

mSet <- preprocessNoob(combined, dyeMethod = "single")
data <- CNV.load(mSet)

I obtained the probes which need to be excluded from my separate analysis for differential probe expression using methylation array analysis package and isolated those probes which were excluded during probe filtering to create the GRange data. I isolate their rowranges from Rgset object. output here the ranges are also of width 1 which does not seem correct.

Finally, when I want to annotate them in conumee, I get the following error. I understand there are NAs in my seqinfo, but I do not know why and how can that be fixed.

anno_combine <- CNV.create_anno(bin_minprobes = 15, bin_minsize=50000,bin_maxsize-5000000, array_type = "450k", chrXY = FALSE, exclude_regions = ep_ranges)

Error in .normarg_seqnames2(seqnames, seqinfo) : 'seqnames' contains sequence names with no entries in 'seqinfo'

I may have done something wrong since I am performing this for the first time, so any help will be appreciated!

Thank you in advance!

[Basti]

Hi, maybe there is a problem with seqnames in your GRanges object, could you give us the output of levels(ep_ranges@seqnames)?

[gs000095]

Hi Bastien, Thank you for your reply,

Here is the output

[Kevin Blighe]

Now on Bioconductor: https://support.bioconductor.org/p/9135472/

[mikat]

Hey gs000095, were you able to solve this error? If yes, may I get some guidance on how to deal with this..

[gs000095]

Hey, so firstly do not combine two arrays when you want to perform CNV analysis using conumee. Secondly, you can find overlapping probes between your annotation data and the RGset and then use this annotation for generating CNVs.