DEXSeqHTML Error

[FuzzyCoder]

We have been able to successfully produce results for a number of comparisons using DEXSeq. However, one comparison is giving us problems as we continuously receive the following error(s) when attempting to create the HTML output of the analysis:

> DEXSeqHTML(ECS_FVBD3012, geneIDs=NULL, FDR=0.01, path="/home/D30B05FVB_12_20120126/FVBD3012DEXSeqReport")
Error in plot.new() : figure margins too large
In addition: Warning messages:
1: In plotDEXSeq(ecs, geneID = gene, FDR = FDR, lwd = 2, expression = opts[1],  :
  This gene contains more than 42 transcripts annotated, only the first 42 will be plotted

All the files appear to be generated in the designated path. However, the page: testForDEU.html only presents the Experimental Design table, not the results table.

We have tried FDR = 0.1, 0.05, and 0.01 and received the same results. Not too many other parameters to play around with.

Any ideas on how to overcome this?

[areyes]

Hi FuzzyCoder,

Could you include the sessionInfo from your R session?

just type:

sessionInfo()

[FuzzyCoder]

Here you go...

R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] Cairo_1.5-1     multicore_0.1-7 DEXSeq_1.0.0    Biobase_2.14.0 

loaded via a namespace (and not attached):
[1] hwriter_1.3  MASS_7.3-16  plyr_1.6     stringr_0.6  tools_2.14.0

[areyes]

Recently, i change the function to fix this bug. In DEXSeq 1.1.6 should work... if not could you send me an ExonCountSet object to give it a closer look???


Thanks!!

[FuzzyCoder]

Sorry for the late response. I've been out of town.

I will try the most current version of DEXSeq and let you know.

Thank you.

[axgraf]

DEXSeqHTML error

I also receive an error creating the HTML output of DEXSeq. I have counted the reads with the python script HTSeq-count and load the files in R with read.HTSeqCounts.

nCores <- 4
counts <- read.HTSeqCounts(files,design,gffFile)
exons <- estimateSizeFactors(counts)
exons <- estimateDispersions(exons, nCores=nCores)
exons <- fitDispersionFunction(exons)
exons <- testForDEU(exons, nCores=nCores)

DEXSeqHTML(exons, geneIds=c("chr19_LOC512110-"), FDR = 0.05 )

[COLOR="Red"]Error in fromw: length(ticks) : NA/NaN argument[/COLOR]

I have 3 replicates for for two conditions (A,B) .
Here is the count table of one of the problematic genes:

Gene	A_rep1	A_rep2	A_rep3	B_rep1	B_rep2	A_rep3 
chr19_LOC512110-	1006	463	157	98	6306	200

SessionInfo:

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages:
[1] hwriter_1.3        multicore_0.1-7    DEXSeq_1.2.0       Biobase_2.16.0    
[5] BiocGenerics_0.2.0

loaded via a namespace (and not attached):
[1] biomaRt_2.12.0 plyr_1.7.1     RCurl_1.91-1   statmod_1.4.14 stringr_0.6   
[6] tools_2.15.1   XML_3.9-4

Any ideas how to solve this problem?

[areyes]

Dear axgraf,

This bug is solved in recent versions of DEXSeq! Could you try to update to the latest version?


Alejandro

[FuzzyCoder]

axgraf-

Are you using dexseq_count.py or a different HT-Seq script for counting? My understanding is that due to DEXSeq's focus on exons, you need to actually use dexseq_count.py for counting; other HT-Seq based scripts won't work.

Alejandro or Simon, Is this still true?

[areyes]

Yes, its true! Thank you for pointing it out!

[axgraf]

I have updated to version 1.3.14 and everything is working perfectly.
There was a typo because I use DESeq and DEXSeq at the moment and I mixed that up.
I use dexseq_count.py for DEXSeq.

Thank you both for your help.

Alex

[parrishdb]

I'm also receiving an error message for the DEXSeqHTML function
"Error in from:length(ticks):NA/NaN argument"

It will create an HTML as an output, but it doesn't contain the actual result table for the results. I am using the DEXSeq package, and using the dexseq_count.py for counting exons. I also have biological replicates for each treatment group. Any suggestions as to why this could be happening?

Below is my session info:

R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

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] stats graphics grDevices utils datasets methods base

other attached packages:
[1] DEXSeq_1.2.0 Biobase_2.16.0 BiocGenerics_0.2.0 BiocInstaller_1.4.7

loaded via a namespace (and not attached):
[1] biomaRt_2.12.0 hwriter_1.3 plyr_1.7.1 RCurl_1.91-1 statmod_1.4.14
[6] stringr_0.6.1 tools_2.15.1 XML_3.9-4

[areyes]

Just update DEXSeq, as Alex did!

I have updated to version 1.3.14 and everything is working perfectly.
There was a typo because I use DESeq and DEXSeq at the moment and I mixed that up.
I use dexseq_count.py for DEXSeq.

Thank you both for your help.

Alex