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:

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

This is what i'm running:

> 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 ...

So, everything looks fine to me. But when i try to create my cds:

> cds <-newCountDataSet(spercysts_vs_embryos, cond )
Error in newCountDataSet(spercysts_vs_embryos, cond) :
  The countData is not integer.

So, if i check what is happening:

> which( is.na(spercysts_vs_embryos), arr.ind=TRUE )
     row col

Any suggestions???
Thanks!


--
Alicia R. Pérez-Porro
PhD candidate

Giribet lab
Department of Organismic and Evolutionary Biology
MCZ labs
Harvard University
26 Oxford St, Cambridge MA 02138
phone: +1 617-496-5308
fax: +1 617-495-5667
www.oeb.harvard.edu/faculty/giribet/

Department of Marine Ecology
Center for Advanced Studies of Blanes (CEAB-CSIC)
C/Accés Cala St. Francesc 14
17300 Blanes, Girona, SPAIN
phone: +34 972 336 101
fax: +34 972 337 806
www.ceab.csic.es

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