[BioC] [Help for DESeq]: Error in lfproc - newsplit: out of vertex space

[Wolfgang Huber]

Dear Imène

are you using a recent version of the software and can you provide a reproducible example?
Please consider the posting guide for this mailing list to see how to write an informative post.

Also, I’d recommend trying your analysis with DESeq2, it has many improvements.

Best wishes
Wolfgang

Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
Genome Biology Unit
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany

T +49-6221-3878823
wolfgang.huber at embl.de
http://www.embl.de/research/units/genome_biology/huber







Il giorno Jul 17, 2014, alle ore 14:26 GMT+2, Imène SENINET <seninet at supagro.inra.fr> ha scritto:

> Hello,
> 
> Thank you for having invovled me in this mailing list :)
> 
> I am trying to measure gene expression differences using RNAseq data. I did several runs using the package R/DESeq. For my testing data I used a *.cvs file, i.e. a table of raw counts containing more than 10800000 reads with 2 conditions (no replicate)
> 
> I get the following error message after calling the function "cds <-estimateDispersions(cds, method='blind',sharingMode='fit-only', fitType='local')":
> 
> -------------------------------------------------------------------------------------------------------------------------------------- 
> /Error in lfproc(x, y, weights = weights, cens = cens, base = base, geth
> = geth,  :
> newsplit: out of vertex space
> In addition: There were 50 or more warnings (use warnings() to see the
> first 50) /
> --------------------------------------------------------------------------------------------------------------------- 
> 
> I've read that this error is related to maxk parameter value in locfit, so I increased it from 300 to 11000000. But the provided solutions did
> not work.
> 
> Would you please help me to find out what wrong with my test?
> 
> Thank you very much and kind regards,
> 
> Imène
> 
> 
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