[BioC] Error DEXSeq

[Alejandro Reyes]

Dear Carriero,

I think you forgot to copy the output of your sessionInfo()?

I think you might be using a very old version of DEXSeq. If so, could 
you please update at least to the current release version of DEXSeq 
(1.10.3), try again and write back if it keeps giving you error messages?

Best regards,
Alejandro

> I have a warning message when I estimate the dipersion parameter. I can't carry on because of some other error messages in the following steps, as I attached below.
> Thanks in advance
>
>   -- output of sessionInfo():
>
> sizeFactors (ecs)
>   7A31.counts  7A32.counts  7A33.counts 46BR1.counts 46BR2.counts 46BR3.counts
>     1.0177858    1.0753635    1.1738656    0.9085247    0.9827212    0.9198726
>> ecs<- estimateDispersions ( ecs )
> Dispersion estimation. (Progress report: one dot per 100 genes)
> ...................................................................................................................................
> Warning messages:
> 1: In .local(object, ...) :
>    Exons with less than 11 counts will be discarded. For more details read the documentation, parameter minCount
> 2: In .local(object, ...) :
>    Genes with more than 70 testable exons will be kicked out of the analysis. For more details read the documentation, parameter maxExon
>> ecs <- fitDispersionFunction(ecs)
> Error in if (sum(log(coefs/oldcoefs)^2) < 0.005) break :
>    missing value where TRUE/FALSE needed
> In addition: Warning messages:
> 1: In glmgam.fit(mm, disps[good], start = coefs) :
>    Too much damping - convergence tolerance not achievable
> 2: In log(coefs/oldcoefs) : NaNs produced
>> head( fData (ecs)$dispBeforeSharing)
> [1] 0.000000e+00 6.003931e-03 4.852941e-03 0.000000e+00 2.771527e-10
> [6] 0.000000e+00
>> ecs at dispFitCoefs
> [1] NA NA
>> head(fData(ecs)$dispFitted)
> [1] NA NA NA NA NA NA
>> plotDispEsts(ecs)
> Error: could not find function "plotDispEsts"
>> ecs<-testForDEU(ecs)
> Error in testForDEU(ecs) :
>    No dispersion values found, call function fitDispersionFunction first.
>
> --
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