Question

我对WGCNA（https://www.rdocumentation.org/packages/WGCNA/versions/1.63/topics/modulePreservation）的modulePreservation函数遇到一些问题。当我将其与multiData数据框（案例组和对照组的基因表达式）一起使用时，出现行号重复的错误。过去，我能够毫无问题地执行此步骤。

（Ps。multiExpr = multiData; control_colors = multiColor）

> modulePreservation(multiExpr, control_colors, dataIsExpr=T, referenceNetworks=1, nPermutations=100, randomSeed=1, quickCor=0, verbose=3, networkType="unsigned")


.checking data for excessive amounts of missing data..
     Flagging genes and samples with too many missing values...
      ..step 1
     Flagging genes and samples with too many missing values...
      ..step 1
  ..unassigned 'module' name: grey 
  ..all network sample 'module' name: gold
  ..calculating observed preservation values
Error in `.rowNamesDF<-`(x, value = value) : 
  duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names': ‘A1CF’, ‘A2M’, ‘AADAC’, ‘AARS’, ‘AASDHPPT’, ‘ABCA12’, ‘ABCA3’, ‘ABCA4’, ‘ABCA8’, ‘ABCB11’, ‘ABCB4’, ‘ABCB9’, ‘ABCC1’, ‘ABCC3’, ‘ABCC6’, ‘ABCD2’, ‘ABCD4’, ‘ABCE1’, ‘ABCF3’, ‘ABCG1’, ‘ABCG2’, ‘ABHD10’, ‘ABHD2’, ‘ABHD4’, ‘ABHD6’, ‘ABI2’, ‘ABL1’, ‘ABL2’, ‘ACAA2’, ‘ACACA’, ‘ACACB’, ‘ACAD10’, ‘ACAD8’, ‘ACADL’, ‘ACADSB’, ‘ACADVL’, ‘ACAN’, ‘ACAP1’, ‘ACAT1’, ‘ACBD3’, ‘ACBD4’, ‘ACCN3’, ‘ACD’, ‘ACE2’, ‘ACHE’, ‘ACIN1’, ‘ACO2’, ‘ACOT7’, ‘ACOT8’, ‘ACOT9’, ‘ACOX3’, ‘ACOXL’, ‘ACPP’, ‘ACR’, ‘ACRV1’, ‘ACSF2’, ‘ACSL3’, ‘ACSL5’, ‘ACSL6’, ‘ACSM3’, ‘ACTB’, ‘ACTC1’, ‘ACTL6B’, ‘ACTL7A’, ‘ACTL8’, ‘ACTN2’, ‘ACTN3’, ‘ACTR1A’, ‘ACTR2’, ‘ACTR3B’, ‘ACTR5’, ‘ACTR8’, ‘ACVR1’, ‘ACVRL1�� [... truncated]

我已经检查了multiExpr文件的row.name和colname，它们都是唯一的值：

sum(duplicated(row.names(multiExpr$Control$data)))
sum(duplicated(row.names(multiExpr$Case$data)))
sum(duplicated(colnames(multiExpr$Control$data)))
sum(duplicated(colnames(multiExpr$Case$data)))

我的R版本是R版本3.5.1（2018-07-02）

Answer 1

似乎是signedKME（）中的错误我已建议在https://slurm.schedmd.com/srun.html

处进行修复

WGCNA-modulePreservation（）中的错误：重复的行。不允许使用名称

1 个答案: