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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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Old 07-21-2011, 12:13 AM   #2
labunit
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Location: Giessen, Germany

Join Date: Sep 2010
Posts: 10
Default

Quote:
Originally Posted by ndeshpan View Post
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
If I remember correctly you should first do the following:

over <- read.delim("C:\\Nandan\\TagSeqExample_top.tab", header=TRUE, stringsAsFactors=TRUE)
conds=c(rep("GZ", 1), rep("DZ", 1))

rownames(over) <- over$gene
over <- over[,-1]

This problem arises because non-numeric values are being passed on (the first colum counts as well). This way only numeric values are present in your count table.
Also check wether there are any empty entries in your table.
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Old 07-21-2011, 03:09 AM   #3
dariober
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Location: Cambridge, UK

Join Date: May 2010
Posts: 311
Default

Hi,
I think the problem is in the count table (over). In your case the first column contains the gene name instead of containing the first count. You should be able to fix it by removing the first column and by assigning gene names to row names (untested):
Code:
over <- read.delim("C:\\Nandan\\TagSeqExample_top.tab", header=TRUE, stringsAsFactors=TRUE)
gene_names<- over[,1]
over<- over[,2:ncol(over)]
rownames(over)<- gene_names
## ...etc
Also, I don't remember the functions of DESeq exactly but I think the vector of conditions should be of the same length as the the number of samples so your conds=c(rep("GZ", 1), rep("DZ", 1)) is incorrect.

Dario
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