[BioC] edgeR warning message when running Trended Dispersion

[Natasha Sahgal]

Dear Prof. Smyth,

Thank you for your reply.

Yes, I eventually did upgrade and realised that the warning message was no longer there.

However, if I may ask a related question. I decided to try the same data below (but as an unpaired analysis) and got an error at the commonTagwiseDisp step. (Latest version of R).

Code:
> y2.filt = y[keep, ]
> design2 = model.matrix(~group)

> y2.filt = estimateCommonDisp(y2.filt, design2, verbose=T)
#Disp = 0.60835 , BCV = 0.78

> y2.filt = estimateTagwiseDisp(y2.filt,design2)
#Error in prior.n/ntags * m0 : non-conformable arrays 

I do not understand the error above. I also tried, the Trened dispersion below and got an error
>y3.filt = y2.filt

>y3.filt = estimateTrendedDisp(y3.filt,design2) 
#Error in estimateTrendedDisp(y3.filt, design2) : 
#  object 'dispersion' not found


Many Thanks,
Natasha

-----Original Message-----
From: Gordon K Smyth [mailto:smyth at wehi.EDU.AU] 
Sent: 16 May 2013 00:01
To: Natasha Sahgal
Cc: Bioconductor mailing list
Subject: edgeR warning message when running Trended Dispersion

Dear Natasha,

Please follow the posting guide

  http://www.bioconductor.org/help/mailing-list/posting-guide/

and "Ensure that you are using the latest Bioconductor release".

Your software is two bioconductor releases behind.

Best wishes
Gordon

> Date: Tue, 14 May 2013 16:58:46 +0000
> From: Natasha Sahgal <nsahgal at well.ox.ac.uk>
> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Subject: [BioC] edgeR warning message when running Trended Dispersion
>
> Dear List,
>
> I am also trying edger on my data (3 groups, 2 reps each).  Bacterial samples.
>
> design
>  condition pair
> 1        Cont    1
> 2        Cont    3
> 3        Trt1    1
> 4        Trt1    3
> 5        Trt2    1
> 6        Trt2    3
>
> However, when I run the following code: I get a warning message and 
> wanted to know it's significance in downstream analysis.

> ----------
> y  = DGEList(counts=gene.counts, group=group)
> str(y)
> y$samples
>
> dim(y$counts) #5578    6
>
> keep = rowSums(cpm(y)>10) >= 3
> table(keep)
> #FALSE  TRUE
> # 1064  4514
>
> y.filt = y[keep, ]
> y.filt$samples$lib.size = colSums(y.filt$counts) y.filt = 
> calcNormFactors(y.filt)
>
> ## Design Matrix
> design = model.matrix(~pair+group)
> colnames(design) = gsub("group","",colnames(design)) design
>
> ## Estimating Dispersion
> y.filt = estimateGLMCommonDisp(y.filt, design, verbose=T) #Disp = 
> 0.03799 , BCV = 0.1949 y.filt = estimateGLMTrendedDisp(y.filt,design)
> #Warning message:
> #In binGLMDispersion(y, design, min.n = min.n, offset = offset, method = method.bin,  :
> #  With 4514 genes and setting the parameter minimum number (min.n) of genes per bin to 500,  there are only 5 bins. Using 5 bins here means that the minimum number of genes in each of the 5 bins is in fact 515. This number of bins and minimum number of genes per bin may not be sufficient for reliable estimation of a trend on the dispersions.
> y.filt = estimateGLMTagwiseDisp(y.filt,design)
> --------------
> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
> [7] LC_PAPER=C                 LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] gdata_2.12.0   WriteXLS_2.3.0 edgeR_2.6.10   limma_3.14.3
>
> loaded via a namespace (and not attached):
> [1] gtools_2.7.0
> -------
>
> Any help, suggestion and advice much appreciated.
>
> Many Thanks,
> Natasha
>

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