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Question: methylumi
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gravatar for Paul Sanfilippo
7.8 years ago by
Paul Sanfilippo70 wrote:
Dear List, I'm attempting my first microarray analysis on a methylation dataset (Illumina Infinium) comprising identical twins (24 -> 12 per array). I thought I'd try the methylumi package - I can import the data, but when I try to Normalise between the two arrays I get an error: > normalizeMethyLumiSet(meth) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "QCdata<-", for signature "MethyLumiSet", "NULL" According to the vignette, QCdata is not required. I know some basics but am not an expert in R. Any help would be appreciated. Thank you. Paul Sanfilippo
ADD COMMENTlink modified 7.8 years ago by Sean Davis21k • written 7.8 years ago by Paul Sanfilippo70
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gravatar for Sean Davis
7.8 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Thu, Jan 14, 2010 at 10:45 PM, Paul Sanfilippo <prseye at="" gmail.com=""> wrote: > Dear List, > > I'm attempting my first microarray analysis on a methylation dataset > (Illumina Infinium) comprising identical twins (24 -> 12 per array). I > thought I'd try the methylumi package - I can import the data, but when I > try to Normalise between the two arrays I get an error: > >> normalizeMethyLumiSet(meth) > Error in function (classes, fdef, mtable) ?: > ?unable to find an inherited method for function "QCdata<-", for signature > "MethyLumiSet", "NULL" > > According to the vignette, QCdata is not required. > > I know some basics but am not an expert in R. > > Any help would be appreciated. Paul, could you do me a quick favor and send along the output of sessionInfo()? Thanks, Sean
ADD COMMENTlink written 7.8 years ago by Sean Davis21k
This is the output: > sessionInfo() R version 2.10.1 Patched (2009-12-29 r50852) x86_64-apple-darwin9.8.0 locale: [1] C/C/en_US/C/C/C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] methylumi_1.0.0 Biobase_2.6.1 ggplot2_0.8.5 digest_0.4.2 [5] reshape_0.8.3 plyr_0.1.9 proto_0.3-8 JGR_1.7-0 [9] iplots_1.1-3 JavaGD_0.5-2 rJava_0.8-1 loaded via a namespace (and not attached): [1] lattice_0.17-26 tools_2.10.1 Thanks Sean. Paul Sean Davis wrote: > On Thu, Jan 14, 2010 at 10:45 PM, Paul Sanfilippo<prseye@gmail.com> wrote: > >> Dear List, >> >> I'm attempting my first microarray analysis on a methylation dataset >> (Illumina Infinium) comprising identical twins (24 -> 12 per array). I >> thought I'd try the methylumi package - I can import the data, but when I >> try to Normalise between the two arrays I get an error: >> >> >>> normalizeMethyLumiSet(meth) >>> >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "QCdata<-", for signature >> "MethyLumiSet", "NULL" >> >> According to the vignette, QCdata is not required. >> >> I know some basics but am not an expert in R. >> >> Any help would be appreciated. >> > > Paul, could you do me a quick favor and send along the output of sessionInfo()? > > Thanks, > Sean > [[alternative HTML version deleted]]
ADD REPLYlink written 7.8 years ago by Paul Sanfilippo70
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