Hi,
I'm starting to use DESeq package since few days, so I'm not very practice yet. I would ask two question.
First ten rows of my data file (TXT format) are presented below:
X6a X6b
ENSG00000000003 20 10
ENSG00000000005 0 0
ENSG00000000419 542 438
ENSG00000000457 468 338
ENSG00000000460 94 81
ENSG00000000938 19604 14802
ENSG00000000971 178 151
ENSG00000001036 559 335
ENSG00000001084 559 312
1st question: Is my data file in the right format?
2nd question:
I execute these commands:
>fuv6a6b<-read.table("C:/Programmi/R/R-devel/library/DESeq/FUV6/rawcount6a-6b.txt",header=TRUE,sep="\t",row.names=1)
>conds <- factor( c( "X6a", "X6b"))
>cds <- newCountDataSet( fuv6a6b, conds )
>cds <- estimateSizeFactors( cds )
>sizeFactors( cds )
>head( counts( cds, normalized=TRUE ) )
So far, so good! But when I execute this command (for estimate Variance):
>cds <- estimateDispersions( cds )
the program print this error message:
Error in rowSums(sapply(tapply((1:ncol(counts))[replicated_sample], factor(conditions[replicated_sample]), :
'x' must be an array of at least two dimensions
How can I solve this problem?
Thanks a lot.
Mattia
I'm starting to use DESeq package since few days, so I'm not very practice yet. I would ask two question.
First ten rows of my data file (TXT format) are presented below:
X6a X6b
ENSG00000000003 20 10
ENSG00000000005 0 0
ENSG00000000419 542 438
ENSG00000000457 468 338
ENSG00000000460 94 81
ENSG00000000938 19604 14802
ENSG00000000971 178 151
ENSG00000001036 559 335
ENSG00000001084 559 312
1st question: Is my data file in the right format?
2nd question:
I execute these commands:
>fuv6a6b<-read.table("C:/Programmi/R/R-devel/library/DESeq/FUV6/rawcount6a-6b.txt",header=TRUE,sep="\t",row.names=1)
>conds <- factor( c( "X6a", "X6b"))
>cds <- newCountDataSet( fuv6a6b, conds )
>cds <- estimateSizeFactors( cds )
>sizeFactors( cds )
>head( counts( cds, normalized=TRUE ) )
So far, so good! But when I execute this command (for estimate Variance):
>cds <- estimateDispersions( cds )
the program print this error message:
Error in rowSums(sapply(tapply((1:ncol(counts))[replicated_sample], factor(conditions[replicated_sample]), :
'x' must be an array of at least two dimensions
How can I solve this problem?
Thanks a lot.
Mattia
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