R WGCNA - error in modulePreservation(): duplicated row.names not allowed

Question

[feltrin88]

I'm having some problems with the modulePreservation function of WGCNA (https://www.rdocumentation.org/packages/WGCNA/versions/1.63/topics/modulePreservation). When I use it with my multiData dataframes (gene expression from case and control groups), I'm having a error of duplicated row.names. In the past, I was able to perform this step with no problems at all.

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]

I already checked the row.names and colnames of my multiExpr files, and all are unique values

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)))

My R version is R version 3.5.1 (2018-07-02)

Answer 1

[Dunja]

Hi,

I have the same problem! Also the newest version of R. Can anyone help?

Answer 2

[peter.langfelder]

Thanks for the report. I confirmed the bug and will fix the function soon.

[fran.harris]

Hi has the bug been fixed? I just want to make sure that I'm not doing something wrong. Thanks!

[farnush.farhadi]

I also have this problem! please let us know when the bug is fixed.

[glgedman]

I just tried to run my re-run my code from months back and ran into this error. Has there been any headway on this? Similar to the initial post, I am running the latest version of R (3.5.1.) and this has not been a problem before.

[ruhinashirin18]

Downloaded the latest resease version WGCNA 1.66, and the bug is fixed. Thanks!

Answer 3

[jjt3f2188]

I'm running WGCNA 1.63 on R 3.4.3 and the following fixed the problem for me:

Before calling modulePreservation:

1. copy the code for the signedKME function (available here: https://rdrr.io/cran/WGCNA/src/R/Functions.R) into a script,
2. replace '..minNSamples' with 4 (which is the value it should have anyway) and
3. redefine the function.

Now modulePreservation() should work.

The error seems to occur here: modulePreservation() calls .modulePreservationInternal() calls .coreCalcForExpr calls signedKME evaluates ..minNSamples