DEXSeq, estimatelog2FoldChanges error

[sahel86]

Hi there,
I ran to a problem with estimatelog2FoldChanges command in DEXSeq.

> Mydata <- estimatelog2FoldChanges(Mydata)
Calculating fold changes. (Progress report: one dot per 100 genes)
Error in do.call(`[[<-`, c(quote(coefIndices), as.list(lvlTbl[i, ]), coefNames[i])) :
[[ ]] subscript out of bounds

I traced the error and find out it is originally made by this line :

> coefIndices <- do.call(`[[<-`, c(quote(coefIndices), as.list(lvlTbl[i, ]), coefNames[i]))

which is a line of DEXSeq:::arrangeCoefs function.

Any ideas what could possibly went wrong here and caused this error?????

Thanks alot,
Sahel

[sahel86]

The issue has been resolved.

[RedLightPanic]

Hi sahel86,

I'm having the same error message when trying to call estimatelog2FoldChanges on my ExonCountSet object.

Could you please explain me how did you solve the issue?

Thanks in advance.

[areyes]

HI RedLightPanic,

Could you include the output of your sessionInfo()?

Alejandro

[RedLightPanic]

Hi Alejandro,

Here is the error message:

> ECS_ecs <- estimatelog2FoldChanges(ECS_ecs)
Error in do.call(`[[<-`, c(quote(coefIndices), as.list(lvlTbl[i, ]), coefNames[i])) :
[[ ]] subscript out of bounds

And here the output of my sessionInfo()

> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] DEXSeq_1.4.0 Biobase_2.18.0 BiocGenerics_0.4.0

loaded via a namespace (and not attached):
[1] biomaRt_2.14.0 hwriter_1.3 plyr_1.7.1 RCurl_1.95-3 statmod_1.4.16
[6] stringr_0.6.1 XML_3.95-0.1

Thanks in advance for your help!