DESeq no recognizing row.names

[alisrpp]

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!

[pbseq]

looks like there'ssome non-integer, have you tried tail(spercysts_vs_embryos) ? Once I had some non-integer in tail
pbseq

[Simon Anders]

Please do not crosspost the same question simultaneously in two forums (SeqAnswers and Bioconductor mailing list).

[alisrpp]

Please do not crosspost the same question simultaneously in two forums (SeqAnswers and Bioconductor mailing list).

Sorry Simon, i was desperate...

[alisrpp]

looks like there'ssome non-integer, have you tried tail(spercysts_vs_embryos) ? Once I had some non-integer in tail
pbseq

> tail(spercysts_vs_embryos)
C4 CRL_2APR10 CRL_1_15JUL11 CRL_2_15JUL11
comp99965_c0_seq1 3 0 11 0
comp99972_c0_seq1 0 0 22 0
comp99988_c0_seq2 0 0 0 0
comp99995_c0_seq1 2 0 0 0
comp999991_c0_seq1 3 0 9 0
comp99999_c0_seq1 5 0 0 0

[muthu545]

Hi,

Perform colSums(spercysts_vs_embryos), to see if there are any decimal vaues
in the sums.

Thanks
--
Muthu

[alisrpp]

Hi,

Perform colSums(spercysts_vs_embryos), to see if there are any decimal vaues
in the sums.

Thanks
--
Muthu

> colSums(spercysts_vs_embryos)
C4 CRL_2APR10 CRL_1_15JUL11 CRL_2_15JUL11
17856472 4152157 27308366 3531719

[muthu545]

Hi,

Is it possible for you to attach the csv file (if in case you do not mind)
in_order to replicate the same problem you encounter.

Thanks
--
Muthu

[pbseq]

it's not very polished , but I'd try:
new_DF =data.frame(cbind(as.integer(spercysts_vs_embryos[,1]),as.integer(spercysts_vs_embryos[,2]),as.integer(spercysts_vs_embryos[,3])))

then to get back to proper colnames:
colnames(new_DF)=c("a","b","c")

[alisrpp]

Hi all,

I discovered that the problem was that RSEM was generating (for some reason that i cannot explain) decimal number in the column of expected count where you are suppose to have only integer numbers... I fixed it with excel (i know that is not a fancy way but i didn't know how to do it).

Thanks,
alisrpp