SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
DESeq2 without biol replicates sisterdot Bioinformatics 23 02-24-2019 08:01 AM
DESeq2 Simon Anders Bioinformatics 123 07-06-2015 01:45 AM
DESeq V DESeq2 sebastion RNA Sequencing 35 10-16-2014 06:04 AM
Getting started with DESeq2 ThePresident Bioinformatics 9 02-27-2014 04:40 PM
DESeq2 SummarizedExperiment help sindrle Bioinformatics 10 10-23-2013 04:20 AM

Reply
 
Thread Tools
Old 01-20-2014, 02:05 AM   #1
choishingwan
Member
 
Location: Hong Kong

Join Date: Feb 2012
Posts: 21
Default Problem with DESeq2 replaceOutliersWithTrimmedMean

Hi there,

I am currently using DESeq2 and have found some NA values in the p-values. From previous post, it was suggested that it is because of a 0 counts in all sample (therefore missing) and because of the Cook's filtering. In the previous version of DESeq2, we can switch off the filtering using nbinomWaldTest(dds, cooksCutoff=FALSE) and this function was gone it the current version. Upon reading the manual, I was found that I can use the function: replaceOutliersWithTrimmedMean to try and get a p-value instead of NA out of DESeq2. However, I've got the following error message:

Error in matrix(rep(trimBaseMean, ncol(dds)), ncol = dds) :
non-numeric matrix extent


Will it has something to do with the warning message I've got from estimateDispersions(dds)?

gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Warning messages:
1: In log(ifelse(y == 0, 1, y/mu)) : NaNs produced
2: step size truncated due to divergence

(I have also applied the cqn normalization to my data.)

Thank you.


My session information
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

other attached packages:
[1] SPIA_2.14.0 KEGGgraph_1.20.0 graph_1.40.1
[4] XML_3.98-1.1 edgeR_3.4.2 limma_3.18.7
[7] DESeq2_1.2.8 RcppArmadillo_0.4.000 Rcpp_0.10.6
[10] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6
[13] BiocGenerics_0.8.0 cqn_1.8.0 quantreg_5.05
[16] SparseM_1.03 preprocessCore_1.24.0 nor1mix_1.1-4
[19] mclust_4.2

loaded via a namespace (and not attached):
[1] annotate_1.40.0 AnnotationDbi_1.24.0 Biobase_2.22.0
[4] DBI_0.2-7 genefilter_1.44.0 grid_3.0.2
[7] lattice_0.20-24 locfit_1.5-9.1 RColorBrewer_1.0-5
[10] RSQLite_0.11.4 stats4_3.0.2 survival_2.37-4
[13] tools_3.0.2 xtable_1.7-1
choishingwan is offline   Reply With Quote
Old 01-21-2014, 04:00 AM   #2
Michael Love
Senior Member
 
Location: Boston

Join Date: Jul 2013
Posts: 333
Default

hi,

Thanks for reporting this. This looks like a simple bug to fix. I will test this and if possible push a new release today.

Mike
Michael Love is offline   Reply With Quote
Old 01-21-2014, 04:10 AM   #3
choishingwan
Member
 
Location: Hong Kong

Join Date: Feb 2012
Posts: 21
Default

Thank you Michael, looking forward to the update
choishingwan is offline   Reply With Quote
Old 01-21-2014, 07:44 AM   #4
Michael Love
Senior Member
 
Location: Boston

Join Date: Jul 2013
Posts: 333
Default

I was able to reproduce, and then fix, this bug. I pushed this fix to v1.2.9 now. It should appear in 1-2 days on Bioc.
Michael Love is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:44 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO