R help - Feb 2009 - Read.table not reading in all columns

Hello,

I am reading in a file called fit2.txt (Limma).  fit2.txt has 38 columns but
when I dim(fit2) I only get 6 columns.  The first column that it does not read
in is df.residual.

fit2<-read.table(fit2,
file="fit2.txt",sep="\t",quote="",comment.char="",as.is=TRUE)

The first few lines of fit2.txt (does not include all 38 columns) looks like
this:

      coefficients.s0vss24 coefficients.s24vss48 coefficients.s48vss96
coefficients.c0vsc24 coefficients.c24vsc48 coefficients.c48vsc96 df.residual
sigma stdev.unscaled.s0vss24
      U179971039 0.058663 0.087575 0.074886 0.099245 -0.18102 0.311904 20
0.176096
      empty1 -0.1296 -0.09105 0.238859 -0.25477 0.063964 0.386198 20 0.34345 
      empty2 0.136259 0.398073 0.158244 0.175756 -0.10171 0.356534 20 0.425968 
      empty3 0.446041 -0.33997 0.345333 0.023821 -0.00783 0.119907 20 0.294745 
      empty4 0.097918 0.168314 0.096333 -0.37584 0.268128 -0.10736 20 0.247398 
      empty5 -0.07256 0.133791 0.086718 0.078185 -0.19707 -0.4144 20 0.342228 
      empty6 0.013663 0.028841 -0.164 0.003989 0.21666 -0.13302 20 0.227787 
      empty7 -0.09123 0.006704 0.357164 -0.23903 -0.01792 0.107122 20 0.309987 
      empty8 0.164526 0.012946 0.130663 0.526142 -0.68847 0.144673 20 0.276618 
      CA054869 0.78055 0.723824 0.491332 0.000452 -0.00143 0.810123 20 0.787196 
      CB490276 -0.43612 0.481221 0.19325 -0.83793 0.611478 0.710366 20 0.800111 
      CA769480 1.201204 -3.45015 -3.58526 -0.28248 -4.21731 -2.75097 20 1.847347


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I'd suggest to make the data available on the web. Then we can take a 
closer look. You or some mail tool in between removed the tabs from the 
message, hence we cannot reproduce in any way.

Best,
Uwe Ligges

Sally wrote:
> Hello,
> 
> I am reading in a file called fit2.txt (Limma).  fit2.txt has 38 columns
but when I dim(fit2) I only get 6 columns.  The first column that it does not
read in is df.residual.
> 
> fit2<-read.table(fit2,
file="fit2.txt",sep="\t",quote="",comment.char="",as.is=TRUE)
> 
> The first few lines of fit2.txt (does not include all 38 columns) looks
like this:
> 
>       coefficients.s0vss24 coefficients.s24vss48 coefficients.s48vss96
coefficients.c0vsc24 coefficients.c24vsc48 coefficients.c48vsc96 df.residual
sigma stdev.unscaled.s0vss24
>       U179971039 0.058663 0.087575 0.074886 0.099245 -0.18102 0.311904 20
0.176096
>       empty1 -0.1296 -0.09105 0.238859 -0.25477 0.063964 0.386198 20
0.34345
>       empty2 0.136259 0.398073 0.158244 0.175756 -0.10171 0.356534 20
0.425968
>       empty3 0.446041 -0.33997 0.345333 0.023821 -0.00783 0.119907 20
0.294745
>       empty4 0.097918 0.168314 0.096333 -0.37584 0.268128 -0.10736 20
0.247398
>       empty5 -0.07256 0.133791 0.086718 0.078185 -0.19707 -0.4144 20
0.342228
>       empty6 0.013663 0.028841 -0.164 0.003989 0.21666 -0.13302 20 0.227787
>       empty7 -0.09123 0.006704 0.357164 -0.23903 -0.01792 0.107122 20
0.309987
>       empty8 0.164526 0.012946 0.130663 0.526142 -0.68847 0.144673 20
0.276618
>       CA054869 0.78055 0.723824 0.491332 0.000452 -0.00143 0.810123 20
0.787196
>       CB490276 -0.43612 0.481221 0.19325 -0.83793 0.611478 0.710366 20
0.800111
>       CA769480 1.201204 -3.45015 -3.58526 -0.28248 -4.21731 -2.75097 20
1.847347
> 
> 
> 	[[alternative HTML version deleted]]
> 
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