[BioC] edgeR: handling missing values with Quantile normalisation

[Paul Leo]

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 at agrf.org.au>
To: 'bioconductor at r-project.org' <bioconductor at 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

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