Attempt to set 'rownames' on an object with no dimensions issues in `champ.DMR`and `champ.SVD`

[Shicheng-Guo]

Hi Yuantian,

An object type warning is found: Attempt to set 'rownames' on an object with no dimensions issues in champ.DMRand champ.SVD

> myDMR <- champ.DMR()
[===========================]
[<<<<< ChAMP.DMR START >>>>>]
-----------------------------
!!! important !!! We just upgrate champ.DMR() function, since now champ.DMP() could works on multiple phenotypes, but ProbeLasso can only works on one DMP result, so if your pheno parameter contains more than 2 phenotypes, and you want to use ProbeLasso function, you MUST specify compare.group=c("A","B"). Bumphunter and DMRcate should not be influenced.

[ Section 1:  Check Input Pheno Start ]

7794 NA are detected in your beta Data Set, which may cause fail or uncorrect of SVD analysis. You may want to impute NA with champ.impute() function first.
  You pheno is factor type.
    Your pheno information contains following groups. >>
    <C>:5 samples.
    <T>:6 samples.

[ Section 1:  Check Input Pheno Done ]

[ Section 2:  Run DMR Algorithm Start ]

<< Find DMR with Bumphunter Method >>
2 cores will be used to do parallel Bumphunter computing.
According to your data set, champ.DMR() detected 10126 clusters contains MORE THAN 7 probes within300 maxGap. These clusters will be used to find DMR.

Error in `[<-.data.frame`(`*tmp*`, list, value = 0.001) :
  new columns would leave holes after existing columns

> champ.SVD(PDFplot=FALSE,Rplot=FALSE)
[===========================]
[<<<<< ChAMP.SVD START >>>>>]
-----------------------------
champ.SVD Results will be saved in ./CHAMP_SVDimages/ .

7794 NA are detected in your beta Data Set, which may cause fail or uncorrect of SVD analysis. You may want to impute NA with champ.impute() function first.
Your beta parameter is data.frame format. ChAMP is now changing it to matrix.
[SVD analysis will be proceed with 485512 probes and 11 samples.]

[ champ.SVD() will only check the dimensions between data and pd, instead if checking if Sample_Names are correctly matched (because some user may have no Sample_Names in their pd file),thus please make sure your pd file is in accord with your data sets (beta) and (rgSet).]

Error in `rownames<-`(`*tmp*`, value = rownames(pd)) :
  attempt to set 'rownames' on an object with no dimensions

sessionInfo ···

sessionInfo() R version 3.6.2 (2019-12-12) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.3 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] grid stats4 parallel stats graphics grDevices utils [8] datasets methods base

other attached packages: [1] doParallel_1.0.16 [2] RnBeads_2.4.0 [3] plyr_1.8.6 [4] methylumi_2.32.0 [5] FDb.InfiniumMethylation.hg19_2.2.0 [6] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [7] GenomicFeatures_1.38.2 [8] reshape2_1.4.4 [9] scales_1.1.1 [10] illuminaio_0.28.0 [11] gridExtra_2.3 [12] gplots_3.1.1 [13] ggplot2_3.3.5 [14] fields_12.5 [15] viridis_0.6.1 [16] viridisLite_0.4.0 [17] spam_2.7-0

···

[YuanTian1991]

Hi Shicheng:

This bug seems un-common. Have you check your matrix have rownames? It looks like an error that row names are missed.

[745757]

I have the same problem. Have you solved it？