Hi Sonika

You can calculate quantile.default independently with the argument
quantile((x, p = q,  na.rm = TRUE)
and pass this value to the main function
this will automatically take care of zeros.

or alternatively you can try other methods ("TMM", "RLE", "quantile") for
calcNormFactors, if that fits in your requirements.

cheers
Alok


On Wed, Aug 31, 2011 at 6:37 AM, Paul Leo <p.leo@uq.edu.au> wrote:

>
> HI Sonika
> It is probably not zero's that are causing the problem but NAs,
>
> Check through the counts array
> to see if it contains  NA's ... someting like..
>
> apply(d$counts,2,function(x) sum(is.na(x)))
>
> should get back all zeros....
>
> probably setting them to 0 is appropriate.
>
>
> Cheers
> Paul
>
>
>
> -----Original Message-----
> From: Sonika Tyagi <Sonika.Tyagi@agrf.org.au>
> To: 'bioconductor@r-project.org' <bioconductor@r-project.org>
> Subject: [BioC] edgeR: handling missing values with Quantile
> normalisation
> Date: Wed, 31 Aug 2011 10:02:26 +1000
>
> Hi there,
>
> I am analysing RNAseq counts using edgeR package. But I am running into
> problems because of 'zero' counts for certain tags in my data.
>
> The code syntax I am using is here:
>
> > targets <- read.delim(file = "Targets.txt", stringsAsFactors = FALSE)
> > targets
>                                  files   group description
> 1  Sample_xx_count.txt.raw control   something
> 2  Sample_xx_count.txt.raw control   something
> 3  Sample_xx_count.txt.raw  Hi_Pos   something
> 4  Sample_xx_count.txt.raw  Hi_Pos   something
> 5  Sample_xx_count.txt.raw control   something
> 6  Sample_xx_count.txt.raw control   something
> 7   ................
>
> d <- readDGE(targets, skip = 0, comment.char = "#")
> d
>
> An object of class "DGEList"
> $samples
>                                 files   group description  lib.size
> norm.factors
> 1 Sample_xx_count.txt.raw control   something 498180513            1
> 2 Sample_xx_count.txt.raw control   something 483775405            1
> 3 Sample_xx_count.txt.raw  Hi_Pos   something 368609647            1
> 4 Sample_xx_count.txt.raw  Hi_Pos   something 617334315            1
> 5 Sample_xx_count.txt.raw control   something 678060765            1
> 13 more rows ...
>
> $counts
>                       1     2     3     4     5     6      7     8     9
>  10     11    12    13    14     15 16    17    18
> Tag1   15923 20323 14867 23098 32484 17223  51579 29578 17408 24097  34470
> 31964 17583 17583  39460  0 30359 25416
> Tag2        700   600   200   695   500  1300   1425  1775   700  1974
> 1300  2371   900   900   1689  0   898  1690
> Tag3      0     0   100     0     0     0      0     0     0     0      0
>   0     0     0    100  0   100     0
> Tag4     74008 58753 51648 65233 93828 71047 117340 90551 55000 70124
> 121393 86106 46197 46197 127290  0 98369 79673
> Tag5     19868 19385 25500 31215 56684 24096  51265 37492 27420 24496
>  32729 24722 24913 24913  50448  0 39755 55829
> 21887 more rows ...
>
>
>  d <- calcNormFactors(d)
> Error in quantile.default(x, p = q) :
>  missing values and NaN's not allowed if 'na.rm' is FALSE
>
> Could someone please suggest how to handle the missing values with edgeR
> normalisation methods ?
>
> Thank you
> Sonika
> -------------------
>
> > sessionInfo()
> R version 2.12.2 (2011-02-25)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
>  LC_MONETARY=English_Australia.1252
> [4] LC_NUMERIC=C                       LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] edgeR_2.0.5  svIDE_0.9-50
>
> loaded via a namespace (and not attached):
> [1] limma_3.6.9   svMisc_0.9-61 tcltk_2.12.2  tools_2.12.2  XML_3.2-0.2
>
>        [[alternative HTML version deleted]]
>
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>



-- 
************************************************************
Alok Kumar Srivastava
Ph.D scholar
Centre of Computational Biology and Bioinformatics
School of Computational and Integrative Sciences
JNU, New Delhi
************************************************************

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