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Question: dmrcate(): Error in `$<-.data.frame`(`*tmp*`, "sig", value = logical(0)) : replacement has 0 rows, data has 1963
0
gravatar for ew17
13 months ago by
ew170
ew170 wrote:

Hi all,

I am using DMRcate to find differentially methylated regions in illumina 450k data. I'm fairly new to R and DMRcate, so I've been following the User Guide example pretty closely. When I get to the dmrcate(myannotation, lambda=1000, C=2) call, I get an error:

"Fitting chr1...

...

Fitting chr8...
Fitting chr9...

Error in `$<-.data.frame`(`*tmp*`, "sig", value = logical(0)) : 

  replacement has 0 rows, data has 1963"

I looked into the source code of the dmrcate method, but I'm still not sure where this error is coming from. The variable "myannotation" is the result from my cpg.annotate() call. I looked up what this error means, and it seems like it's because "sig" is not a variable in the dataset, but I'm not sure where the dataset is being constructed in the dmrcate method. Anyway, how should I go about addressing this issue? Please let me know if I should also provide any other information to make this easier to understand. 

Thanks in advance,

Eugene 

 

 

ADD COMMENTlink modified 10 months ago by Tim Peters60 • written 13 months ago by ew170
0
gravatar for Tim Peters
13 months ago by
Tim Peters60
Australia
Tim Peters60 wrote:

Hi Eugene,

Can you post a traceback() on this error and then a sessionInfo() please?

Cheers,

Tim 

ADD COMMENTlink written 13 months ago by Tim Peters60

Sorry about the delay; I didn't see your response until now. The output of traceback() is:

4: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", 
       "replacement has %d rows, data has %d"), N, nrows), domain = NA)
3: `$<-.data.frame`(`*tmp*`, "sig", value = logical(0))
2: `$<-`(`*tmp*`, "sig", value = logical(0))
1: dmrcate(myannotation, lambda = 1000, C = 2)

ADD REPLYlink written 12 months ago by ew170
0
gravatar for ew17
12 months ago by
ew170
ew170 wrote:

sessionInfo():

R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.2 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] splines   stats4    parallel  stats     graphics  grDevices utils     datasets 
 [9] methods   base     

loaded via a namespace (and not attached):
 [1] nlme_3.1-128             bitops_1.0-6             matrixStats_0.51.0      
 [4] RColorBrewer_1.1-2       tools_3.2.2              doRNG_1.6               
 [7] nor1mix_1.2-2            R6_2.2.0                 rpart_4.1-10            
[10] Hmisc_3.17-4             Gviz_1.14.7              DBI_0.5-1               
[13] colorspace_1.2-7         nnet_7.3-12              gridExtra_2.2.1         
[16] base64_2.0               chron_2.3-47             preprocessCore_1.32.0   
[19] pkgmaker_0.22            rtracklayer_1.30.4       scales_0.4.0            
[22] genefilter_1.52.1        quadprog_1.5-5           stringr_1.1.0           
[25] digest_0.6.10            Rsamtools_1.22.0         foreign_0.8-67          
[28] R.utils_2.4.0            illuminaio_0.12.0        siggenes_1.44.0         
[31] GEOquery_2.36.0          dichromat_2.0-0          htmltools_0.3.5         
[34] BSgenome_1.38.0          limma_3.26.9             htmlwidgets_0.7         
[37] RSQLite_1.0.0            shiny_0.14.1             jsonlite_1.1            
[40] mclust_5.2               BiocParallel_1.4.3       gtools_3.5.0            
[43] acepack_1.4.0            R.oo_1.20.0              dplyr_0.5.0             
[46] VariantAnnotation_1.16.4 RCurl_1.95-4.8           magrittr_1.5            
[49] Formula_1.2-1            futile.logger_1.4.3      Matrix_1.2-7.1          
[52] Rcpp_0.12.7              munsell_0.4.3            R.methodsS3_1.7.1       
[55] stringi_1.1.2            MASS_7.3-45              zlibbioc_1.16.0         
[58] plyr_1.8.4               grid_3.2.2               multtest_2.26.0         
 

ADD COMMENTlink modified 12 months ago • written 12 months ago by ew170

Sorry about the separation; the 5000 character limit kept having issues.

[61] GenomicFeatures_1.22.13  annotate_1.48.0          knitr_1.14              
[64] beanplot_1.2             igraph_1.0.1             rngtools_1.2.4          
[67] corpcor_1.6.8            reshape2_1.4.2           codetools_0.2-15        
[70] biomaRt_2.26.1           mixOmics_6.1.1           futile.options_1.0.0    
[73] XML_3.98-1.4             biovizBase_1.18.0        latticeExtra_0.6-28     
[76] lambda.r_1.1.9           data.table_1.9.6         httpuv_1.3.3            
[79] gtable_0.2.0             openssl_0.9.4            tidyr_0.6.0             
[82] reshape_0.8.6            assertthat_0.1           ggplot2_2.1.0           
[85] mime_0.5                 xtable_1.8-2             survival_2.39-5         
[88] tibble_1.2               GenomicAlignments_1.6.3  AnnotationDbi_1.32.3    
[91] registry_0.3             ellipse_0.3-8            cluster_2.0.5           
[94] rgl_0.96.0   

ADD REPLYlink written 12 months ago by ew170
0
gravatar for Tim Peters
12 months ago by
Tim Peters60
Australia
Tim Peters60 wrote:

Hi Eugene,

DMRcate_1.6.53 is a fairly old version, more than a year old in fact. I think there were a couple of bugs in it that have been ironed out since. Please upgrade to the newest version https://www.bioconductor.org/packages/release/bioc/html/DMRcate.html and hopefully you'll find it works properly.

Cheers,

TIm

 

ADD COMMENTlink written 12 months ago by Tim Peters60

Hey, did you ever get an fix for the error? I am using the most recent version (the one mentioned above) and stuck with the same error. 

ADD REPLYlink written 12 months ago by hrishi27n0
0
gravatar for Tim Peters
12 months ago by
Tim Peters60
Australia
Tim Peters60 wrote:

This error could be down to one of a number of things:

 

1) First look if you still have your SNP probes in your data matrix. The rownames will begin with "rs" instead of "cg". Remove them.

 

2) If there are any NAs in your data matrix then nsig will be NA instead of a number. Get rid of any rows that have NAs.

 

3) If the variance is exactly zero for any of your rows (i.e. all values are identical) then limma will throw this error too. Check for rows that whose values are all the same.

 

If you're still having trouble after trying these please send me your R workflow and I will have a look at it.

 

Good luck,

Tim

ADD COMMENTlink written 12 months ago by Tim Peters60
0
gravatar for Yuan Tian
11 months ago by
Yuan Tian70
London
Yuan Tian70 wrote:

Hello  Eugene,Tim:

I encountered the same error report as well. And I checked it in DMRcate code (I am using version 1.10.0):

I think there is a small bug in dmrcate() function. In the function, pcutoff parameter is used to select significant differential CpGs. It can be assigned as value or "fdr". The default value is "fdr", which means insides dmrcate() function, a numeric value of cutoff will be generated. Or we can assign a value to pcutoff.

The bug lies on line 50 : object$sig <- object$fdr <= pcutoff. This line of code will find all CpG with fdr-adjusted p value smaller then pcutoff. But if there is no CpG fulfill this condition, the error would happen.

So the easiest way to solve this error is to assign pcutoff to a higher value. (Actually I think fdr adjust is very strict, maybe a 0.1 cutoff is also acceptable). I tried to assign pcutoff parameter value as 0.1 and my function works well then. But how to adjust pcutoff parameter is totally depends on researchers' research, I am not sure 0.1 is a suitable value.

Tim, maybe you can slightly modify the code in this line. And return a message to users so that we can adjust pcutoff parameter ourselves.

Best

Yuan Tian

ADD COMMENTlink written 11 months ago by Yuan Tian70
0
gravatar for Tim Peters
10 months ago by
Tim Peters60
Australia
Tim Peters60 wrote:

Hi Yuan and Eugene,

Thanks for the feedback, that is indeed a bug. It should be fixed in the git now and propagated to Bioconductor in 48 hours. 

To clarify, it is highly recommended that the thresholding be tuned using the fdr argument in cpg.annotate(). If there are no CpGs below this threshold, there should be a message stating this. 

ADD COMMENTlink written 10 months ago by Tim Peters60
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