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Urmi Trivedi

2007-Aug-07 13:33 UTC

[R] Error in as.double.default(x) : (list) object cannot be coerced to 'double'

Dear experts,

I have in all 14 matrices which stands for gene expression divergence and 14
matrices which stands for gene sequence divergence. I have tried joining them by
using the concatanation function giving

SequenceDivergence <- c(X1,X2,X3,X4,X5,X6,X7,X8,X9,X10,X11,X12,X13,X14)
ExpressionDivergence <- c(Y1,Y2,Y3,Y4,Y5,Y6,Y7,Y8,Y9,Y10,Y11,Y12,Y13,Y14) 

where X1,X2..X14 are the expression matrices containing r-values and 
Y1,Y2..Y14 are the ones with patristic distances

Now, I want to plot SequenceDivergence vs. Expression Divergence

Tried doing that using plot (Sequence Divergence vs. Expression Divergence)

But then getting the error 

 Error in as.double.default(x) : (list) object cannot be coerced to
'double'

Note: The diagonal values for X1 was neglected as its seems to give some bias in
my results. Code to derive X1,X2,X3..and Y1,Y2,Y3 is given as:
> EDant <- read.table("C:/ant.txt",sep="\t")
> ED1 <- as.matrix(EDant)
> X1 <- lapply(1:ncol(ED15), function(a) ED15[-a, a]) # to neglect
diagonal values
I am attaching couple of matrices for your reference. ANT.txt is X1 after
deleting the diagnol values, similarly,ANTEXP.TXT is Y1,  apetella.txt is X2 and
apetellaexp.txt is Y2

I tried reading R-manual and other sources but have'nt cracked it yet. Can
anyone please help me regarding that?
 
 Thanks very much
 
 Yours sincerely,
 
 Urmi Trivedi. 


       
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Petr PIKAL

2007-Aug-08 09:54 UTC

head link

[R] Odp: Error in as.double.default(x) : (list) object cannot be coerced to 'double'

Hi

Far from beeing an expert I can decide from your post that you probably 
mix R objects matrix x data frame x list. All of them have specific 
features and you sometimes cannot convert one to another easily. See what 
your objects are and how they look like by e.g.

str(X1)
or mode or typeof

I suspect that your X are lists and using c(some lists) result again into 
list.

Plot expect x and y values usually as vectors but there are plot methods 
for other objects (data.frames, functions, ...) 

Best starting point would be help page for plot.

Regards
Petr


r-help-bounces at stat.math.ethz.ch napsal dne 07.08.2007 15:33:41:
> Dear experts,
> 
> I have in all 14 matrices which stands for gene expression divergence 
and 14 > matrices which stands for gene sequence divergence. I have tried joining 
them > by using the concatanation function giving
> 
> SequenceDivergence <- c(X1,X2,X3,X4,X5,X6,X7,X8,X9,X10,X11,X12,X13,X14)
> ExpressionDivergence <- 
c(Y1,Y2,Y3,Y4,Y5,Y6,Y7,Y8,Y9,Y10,Y11,Y12,Y13,Y14) > 
> where X1,X2..X14 are the expression matrices containing r-values and 
> Y1,Y2..Y14 are the ones with patristic distances
> 
> Now, I want to plot SequenceDivergence vs. Expression Divergence
> 
> Tried doing that using plot (Sequence Divergence vs. Expression 
Divergence)> 
> But then getting the error 
> 
>  Error in as.double.default(x) : (list) object cannot be coerced to 
'double'> 
> Note: The diagonal values for X1 was neglected as its seems to give some 
bias > in my results. Code to derive X1,X2,X3..and Y1,Y2,Y3 is given as:
> 
> > EDant <- read.table("C:/ant.txt",sep="\t")
> > ED1 <- as.matrix(EDant)
> > X1 <- lapply(1:ncol(ED15), function(a) ED15[-a, a]) # to neglect 
diagonal values > 
> I am attaching couple of matrices for your reference. ANT.txt is X1 
after > deleting the diagnol values, similarly,ANTEXP.TXT is Y1,  apetella.txt 
is X2 and > apetellaexp.txt is Y2
> 
> I tried reading R-manual and other sources but have'nt cracked it yet. 
Can > anyone please help me regarding that?
> 
>  Thanks very much
> 
>  Yours sincerely,
> 
>  Urmi Trivedi. 
> 
> 
> 
> ---------------------------------
>  Once upon a time there was 1 GB storage in your inbox. Click here for 
happy > ending.0   1.21133   1.420221   1.499358   1.475149   1.513886 1.608816  
1.> 675916   1.859038   1.992958   2.420123   2.309414   2.413222
> 1.21133   0   1.463585   1.542722   1.518513   1.55725   1.65218 1.71928 
 > 1.902402   2.036322   2.463487   2.352778   2.456586
> 1.420221   1.463585   0   1.418619   1.39441   1.433147   1.528077 
1.595177 > 1.778299   1.912219   2.339384   2.228675   2.332483
> 1.499358   1.542722   1.418619   0   0.931235   0.969972   1.354498 
1.421598> 1.60472   1.73864   2.165805   2.055096   2.158904
> 1.475149   1.518513   1.39441   0.931235   0   0.206013   1.330289 
1.397389 > 1.580511   1.714431   2.141596   2.030887   2.134695
> 1.513886   1.55725   1.433147   0.969972   0.206013   0   1.369026 
1.436126 > 1.619248   1.753168   2.180333   2.069624   2.173432
> 1.608816   1.65218   1.528077   1.354498   1.330289   1.369026   0 
0.604972 > 1.537696   1.671616   2.098781   1.988072   2.09188
> 1.675916   1.71928   1.595177   1.421598   1.397389   1.436126 0.604972  
0 > 1.604796   1.738716   2.165881   2.055172   2.15898
> 1.859038   1.902402   1.778299   1.60472   1.580511   1.619248 1.537696  
1.> 604796   0   1.09121   1.968427   1.857718   1.961526
> 1.992958   2.036322   1.912219   1.73864   1.714431   1.753168 1.671616  
1.> 738716   1.09121   0   2.102347   1.991638   2.095446
> 2.420123   2.463487   2.339384   2.165805   2.141596   2.180333 2.098781 
 > 2.165881   1.968427   2.102347   0   1.128701   1.232509
> 2.309414   2.352778   2.228675   2.055096   2.030887   2.069624 1.988072 
 > 2.055172   1.857718   1.991638   1.128701   0   0.91546
> 2.413222   2.456586   2.332483   2.158904   2.134695   2.173432 2.09188  
2.> 15898   1.961526   2.095446   1.232509   0.91546   0
> 1   -0.046373   -0.033044   0.003902   0.466827   0.389327   0.131989 
-0.> 063346   -0.118093   0.016386   -0.140215   0.34511   0.233074
> -0.046373   1   0.000717   0.832227   0.077053   -0.106815   -0.050838 
0.> 936431   0.297387   0.031358   -0.127265   0.31245   -0.053169
> -0.033044   0.000717   1   0.011265   -0.018602   -0.023669   -0.028744  
-0.> 007588   0.148827   -0.007067   0.005362   -0.029172   -0.017367
> 0.003902   0.832227   0.011265   1   0.071247   -0.101225   0.097117 0.
> 829167   0.294396   0.017809   -0.129199   0.278831   -0.106427
> 0.466827   0.077053   -0.018602   0.071247   1   0.078241   0.140679 0.
> 070069   0.055744   0.013194   -0.196092   -0.027692   0.028857
> 0.389327   -0.106815   -0.023669   -0.101225   0.078241   1   0.140146 
-0.> 086806   0.079   0.194904   0.068378   0.213288   0.194006
> 0.131989   -0.050838   -0.028744   0.097117   0.140679   0.140146   1 
-0.> 075079   0.137652   0.065127   -0.072768   -0.120751   -0.101777
> -0.063346   0.936431   -0.007588   0.829167   0.070069   -0.086806 
-0.075079> 1   0.312154   0.023108   -0.122502   0.331402   -0.042298
> -0.118093   0.297387   0.148827   0.294396   0.055744   0.079   0.137652 
  0.> 312154   1   0.300515   -0.178301   0.033663   -0.057139
> 0.016386   0.031358   -0.007067   0.017809   0.013194   0.194904 
0.065127 > 0.023108   0.300515   1   -0.096451   0.033663   -0.039394
> -0.140215   -0.127265   0.005362   -0.129199   -0.196092   0.068378 -0.
> 072768   -0.122502   -0.178301   -0.096451   1   -0.01748   0.253667
> 0.34511   0.31245   -0.029172   0.278831   -0.027692   0.213288 
-0.120751 > 0.331402   0.033663   0.033663   -0.01748   1   0.201202
> 0.233074   -0.053169   -0.017367   -0.106427   0.028857   0.194006 
-0.101777> -0.042298   -0.057139   -0.039394   0.253667   0.201202   1
> 0   1.936157   2.266211   3.072091   3.273938   3.486342
> 1.936157   0   2.174716   2.980596   3.182443   3.394847
> 2.266211   2.174716   0   2.935008   3.136855   3.349259
> 3.072091   2.980596   2.935008   0   1.888593   2.100997
> 3.273938   3.182443   3.136855   1.888593   0   1.383438
> 3.486342   3.394847   3.349259   2.100997   1.383438   0
> 1   0.179826   -0.009544   -0.3113   0.149974   -0.204895
> 0.179826   1   0.100759   0.276355   0.098351   0.221849
> -0.009544   0.100759   1   -0.128468   0.032579   -0.212893
> -0.3113   0.276355   -0.128468   1   -0.118107   0.780792
> 0.149974   0.098351   0.032579   -0.118107   1   -0.120811
> -0.204895   0.221849   -0.212893   0.780792   -0.120811   1
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R help - Aug 2007 - Error in as.double.default(x) : (list) object cannot be coerced to 'double'

[R] Error in as.double.default(x) : (list) object cannot be coerced to 'double'

[R] Odp: Error in as.double.default(x) : (list) object cannot be coerced to 'double'

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