Hi,
I'm trying to use DESeq to know the differential expressed genes of my datasets and i'm encountering that DESeq is not recognizing my row.names so i can't create my cds.
My .csv input file looks like:
This is what i'm running:
So, everything looks fine to me. But when i try to create my cds:
So, if i check what is happening:
Any suggestions???
Thanks!
I'm trying to use DESeq to know the differential expressed genes of my datasets and i'm encountering that DESeq is not recognizing my row.names so i can't create my cds.
My .csv input file looks like:
Code:
transcript_id,C4,CRL_2APR10,CRL_1_15JUL11,CRL_2_15JUL11 comp1000201_c0_seq1,5.00,0.00,0.00,0.00 comp1000297_c0_seq1,7.00,0.00,0.00,0.00 comp100036_c0_seq1,0.00,0.00,0.00,0.00 comp10003_c1_seq1,2.00,0.00,0.00,0.00 comp100041_c0_seq1,3.00,0.00,0.00,0.00 comp100041_c0_seq2,0.00,0.00,0.00,0.00 comp100041_c0_seq3,0.00,0.00,0.00,0.00 comp100051_c0_seq1,0.00,0.00,0.00,0.00 comp1000890_c0_seq1,3.00,0.00,0.00,0.00
Code:
> spercysts_vs_embryos = read.csv ( + file.choose(), + header = TRUE, + row.names=1, + sep = ",", + dec = ".") > head(spercysts_vs_embryos) C4 CRL_2APR10 CRL_1_15JUL11 CRL_2_15JUL11 comp1000201_c0_seq1 5 0 0 0 comp1000297_c0_seq1 7 0 0 0 comp100036_c0_seq1 0 0 0 0 comp10003_c1_seq1 2 0 0 0 comp100041_c0_seq1 3 0 0 0 comp100041_c0_seq2 0 0 0 0 >cond = factor(c("SP", "SP", "EB", "EB")) > spercysts_vs_embryosDesign = data.frame( + row.names = colnames( spercysts_vs_embryos ), + condition = c( "SP", "SP", "EB", "EB" ), + libType = c( "paired-end", "paired-end", "paired-end", "paired-end" ) ) > spercysts_vs_embryosDesign condition libType C4 SP paired-end CRL_2APR10 SP paired-end CRL_1_15JUL11 EB paired-end CRL_2_15JUL11 EB paired-end > str(spercysts_vs_embryos) 'data.frame': 307048 obs. of 4 variables: $ C4 : num 5 7 0 2 3 0 0 0 3 0 ... $ CRL_2APR10 : num 0 0 0 0 0 0 0 0 0 0 ... $ CRL_1_15JUL11: num 0 0 0 0 0 0 0 0 0 10 ... $ CRL_2_15JUL11: num 0 0 0 0 0 0 0 0 0 3 ...
Code:
> cds <-newCountDataSet(spercysts_vs_embryos, cond ) Error in newCountDataSet(spercysts_vs_embryos, cond) : The countData is not integer.
Code:
> which( is.na(spercysts_vs_embryos), arr.ind=TRUE ) row col
Thanks!
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