If i do:

>which( spercysts_vs_embryos != round (spercysts_vs_embryos),
     arr.ind=TRUE )

I get:

comp203811_c0_seq3    44259   1
comp203811_c0_seq4    44260   1
comp203818_c0_seq2    44266   1
comp203818_c0_seq4    44268   1
comp203827_c0_seq2    44281   1
comp203827_c0_seq3    44282   1
comp203827_c0_seq7    44286   1
comp203828_c0_seq1    44287   1
 [ reached getOption("max.print") -- omitted 166743 rows ]


If i do:


>which(round(spercysts_vs_embryos) != spercysts_vs_embryos), arr.ind=TRUE)


I get:


Error: unexpected ',' in "which(round(spercysts_vs_embryos) !=
spercysts_vs_embryos),"



On Fri, May 24, 2013 at 4:51 PM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:

> Hi Alicia,
>
> On Fri, May 24, 2013 at 2:38 PM, Alicia R. Pérez-Porro
> <alicia.r.perezporro@gmail.com> wrote:
> > 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:
>
> Everything isn't fine :-) Your columns should be integers, not just
> "numeric". If you look at the source code of `newCountDataSet`, you'll
> see right at the very top:
>
>     countData <- as.matrix(countData)
>     if (any(round(countData) != countData))
>         stop("The countData is not integer.")
>
> Which looks like the error you are getting here:
>
> >> cds <-newCountDataSet(spercysts_vs_embryos, cond )
> > Error in newCountDataSet(spercysts_vs_embryos, cond) :
> >   The countData is not integer.
>
> So it's not that you have NA's in your data.frame, but your first
> problem is that the numbers you are using for your count matrix are
> not rounding to themselves, which is a quick/easy way to check that
> they aren't whole numbers, as you would expect by count data, and
> DESeq requires count data.
>
> So, instead of checking for NA here:
>
> > So, if i check what is happening:
> >
> >> which( is.na(spercysts_vs_embryos), arr.ind=TRUE )
> >      row col
>
> You might try to check which numbers are suspect:
>
> R> which(round(spercysts_vs_embryos) != spercysts_vs_embryos),
> arr.ind=TRUE)
>
> HTH,
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>

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