Error in preprocessQuantile and preprocessFunnorm

michaelnoe commented 5 years ago

I get an error while running preprocessFunnorm: [preprocessFunnorm] Background and dye bias correction with noob [preprocessFunnorm] Mapping to genome [preprocessFunnorm] Quantile extraction Error: number of cluster centres must lie between 1 and nrow(x)

and something similar for preprocessQuantile: [preprocessQuantile] Mapping to genome. Error: number of cluster centres must lie between 1 and nrow(x)

I only ran the basic code (no subsetting of the data like in the previous case): targets <- read.metharray.sheet(getwd()) RGset <- read.metharray.exp(targets = targets) mdata1 <- preprocessFunnorm(RGset) mdata2<- preprocessQuantile(RGset)

kasperdanielhansen commented 5 years ago

How many samples, what is the sex distribution; print the RGset object and paste result here and finally what is R/minfi versions.

On Tue, Feb 5, 2019 at 12:19 PM michaelnoe notifications@github.com wrote:

I get an error while running preprocessFunnorm: [preprocessFunnorm] Background and dye bias correction with noob [preprocessFunnorm] Mapping to genome [preprocessFunnorm] Quantile extraction Error: number of cluster centres must lie between 1 and nrow(x)

and something similar for preprocessQuantile: [preprocessQuantile] Mapping to genome. Error: number of cluster centres must lie between 1 and nrow(x)

I only ran the basic code (no subsetting of the data like in the previous case): 'targets <- read.metharray.sheet(getwd()) 'RGset <- read.metharray.exp(targets = targets) mdata1 <- preprocessFunnorm(RGset) mdata2<- preprocessQuantile(RGset)

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michaelnoe commented 5 years ago

It's two samples: 1 woman and 1 man: the RGset is: class: RGChannelSet dim: 1051815 2 metadata(0): assays(2): Green Red rownames(1051815): 1600101 1600111 ... 99810990 99810992 rowData names(0): colnames(2): 203219720041_R07C01 203219720041_R08C01 colData names(9): Sample_Name Sample_Well ... Basename filenames Annotation array: IlluminaHumanMethylationEPIC annotation: ilm10b4.hg19

my setup: platform x86_64-apple-darwin15.6.0 arch x86_64 os darwin15.6.0 system x86_64, darwin15.6.0 status major 3 minor 5.2 year 2018 month 12 day 20 svn rev 75870 language R version.string R version 3.5.2 (2018-12-20) nickname Eggshell Igloo

minfi: version 1.28.3

michaelnoe commented 5 years ago

It's probably not associated with the setup, since I just tried it on the jhpce-cluster and it gives the same error...

iranmdl commented 1 month ago

I am having the same issue, any updates?

RGSet

class: RGChannelSet
dim: 622399 2
metadata(0):
assays(2): Green Red
rownames(622399): 10600313 10600322 ... 74810490 74810492
rowData names(0):
colnames(2): 5723646052_R02C02 5723646052_R04C01
colData names(13): Sample_Name Sample_Well ... Basename filenames
Annotation
  array: IlluminaHumanMethylation450k
  annotation: ilmn12.hg19

RijndertAriese commented 1 month ago

Hi,

I also encounter the same issue, could someone shed some light on this?

My RGSet:

class: RGChannelSet 
dim: 1051943 2 
metadata(0): 
assays(2): Green Red(1051943): 1600101 1600111 ... 99810990 99810992
rowData names(0):
colnames(2): BRO.Tumor BRO.Healthy
colData names(7): GSM_ID Sample_Name ... Basename filenames
Annotation
  array: IlluminaHumanMethylationEPIC
  annotation: ilm10b4.hg19

When I run preprocessQuantile(rgSet) I get Error: number of cluster centres must lie between 1 and nrow(x)

Any help would be appreciated

hansenlab / minfi

Error in preprocessQuantile and preprocessFunnorm #180