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Old 07-20-2011, 11:45 PM   #1
ndeshpan
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Location: Sydney

Join Date: Nov 2009
Posts: 29
Default DESeq input table upload

Hi,

I am new to DESeq (R version 2.13.1) and am trying to upload a tab delimited file.. (I am using the sample file "TagSeqExample.tab"), but I am getting an error..

==================================================
> library( DESeq )
Loading required package: Biobase

Welcome to Bioconductor

Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: locfit
Loading required package: akima
Loading required package: lattice
locfit 1.5-6 2010-01-20
Warning messages:
1: '.readRDS' is deprecated.
Use 'readRDS' instead.
See help("Deprecated")
2: '.readRDS' is deprecated.
Use 'readRDS' instead.
See help("Deprecated")
3: '.readRDS' is deprecated.
Use 'readRDS' instead.
See help("Deprecated")
> over <- read.delim("C:\\Nandan\\TagSeqExample_top.tab", header=TRUE, stringsAsFactors=TRUE)
> conds=c(rep("GZ", 1), rep("DZ", 1))
> head(over)
gene T1a T1b T2 T3 N1 N2
1 Gene_00001 0 0 2 0 0 1
2 Gene_00002 20 8 12 5 19 26
3 Gene_00003 3 0 2 0 0 0
4 Gene_00004 75 84 241 149 271 257
5 Gene_00005 10 16 4 0 4 10
6 Gene_00006 129 126 451 223 243 149
> conds=c(rep("GZ", 1), rep("DZ", 1))
> cds <- newCountDataSet( over, conds )
Error in round(countData) : Non-numeric argument to mathematical function
==================================================

I tried my dataset (tab de-limited file) but with the same results.. I distinctly remember my tab separated file getting uploaded fine with the previous version of DeSeq (however I need to use this version to use a few new methods)

I have confirmed that the columns contain only numeric characters

Can anyone pint me in the right direction?

cheers,

Nandan
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