[Bioc-sig-seq] A question of edgeR DGEList() - no norm.factors generated

[Davis McCarthy]

Hi Kyunghee

>From the output that you have provided I can't diagnose what is going on here. I don't know what versions of R and edgeR you are using, and you have not provided information about the error that you are getting from calcNormFactors() (output missing below, no traceback() ). Please check the posting guide here: http://www.bioconductor.org/help/mailing-list/posting-guide/

I would suggest updating to the latest versions of R and edgeR and trying again. If the problem persists then please provide some more information about the error.

Cheers
Davis



On Mar 30, 2011, at 2:02 PM, Kyunghee Park wrote:

> Hi!
> 
> I have a problem using edgeR packages, especially DGEList() function.
> Though there's no error messege when I run DGEList(), I don't have
> "norm.factors" in cds$samples.
> And I can't run calcNormFactors(), either. (It was same that I added
> norm.factors<-1 in cds$samples dataset manually and then run
> calcNormFactors().)
> If you guys help to fix it, it'll be very helpful.
> 
> Thank you in advance.
> Kyunghee Park
> 
> ===
>> conds
> [1] "other"  "other"  "other"  "breast" "breast" "other"  "other"  "breast"
> [9] "breast"
>> 
> cds<-DGEList(counts=mirna.count.matrix,group=conds,lib.size=NULL,genes=NULL,remove.zeros=FALSE)
> Calculating library sizes from column totals.
>> cds
> An object of class "DGEList"
> $samples
>           group lib.size
> SRR029124  other   970218
> SRR029125  other  1500254
> SRR029126  other  1280521
> SRR029127 breast   947041
> SRR029128 breast   737793
> SRR029129  other  1531409
> SRR029130  other   908642
> SRR029131 breast  1679689
> SRR029132 breast  1143424
> 
> $counts
>             SRR029124 SRR029125 SRR029126 SRR029127 SRR029128 SRR029129
> hsa-let-7a-1     38631     30886      4725         4     30986      1677
> hsa-let-7c        1220      3154      8196      2504      5944       121
> hsa-let-7d         680       286     43931         0       643         2
> hsa-let-7f-1     38631      1026     46053       439     30986         0
> hsa-let-7f-2        29      1344        12      2336      1753      2079
>             SRR029130 SRR029131 SRR029132
> hsa-let-7a-1      1055      1106         2
> hsa-let-7c          36         4         2
> hsa-let-7d         236         2      9865
> hsa-let-7f-1         2         6         1
> hsa-let-7f-2       396       745         7
> 548 more rows ...
> 
> $allZeros
> hsa-let-7a-1   hsa-let-7c   hsa-let-7d hsa-let-7f-1 hsa-let-7f-2
>       FALSE        FALSE        FALSE        FALSE        FALSE
> 548 more elements ...
>> cds<-calcNormFactors(cds)
> ?
> ===
> 
> 	[[alternative HTML version deleted]]
> 
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------------------------------------------------------------------------
Davis J McCarthy
Research Technician
Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Vic 3052, Australia
dmccarthy at wehi.edu.au
http://www.wehi.edu.au




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