How to resolve the following error: (list) object cannot be coerced to type 'double'

[Jason Love]

Hello,
I'd like to test a significance of two variables in their correlation using
rcorr, which gave me an error of format incompatibility.
Below are the lines that I typed in the R window and let me know if anyone
knows how to resolve this.

Var=read.csv("03apr10ab_corr_matrix_in_overlaps.csv",header=F)
colnames(Var)=c("D Prime","T statistics")

         D Prime    T statistics
1    1.7234e-01     4.926800
2    1.4399e-01     2.892000
3    1.4626e-01     2.642800
4    3.5147e-02     1.112400
5    5.8957e-02     2.723700


rcorr(Var, type="pearson")

Error in storage.mode(x) <- if (.R.) "double" else "single" :
  (list) object cannot be coerced to type 'double'

        [[alternative HTML version deleted]]

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[Michael Weylandt]

On Wed, Sep 12, 2012 at 4:04 PM, Jason Love <[hidden email]> wrote:

> Hello,
> I'd like to test a significance of two variables in their correlation using
> rcorr, which gave me an error of format incompatibility.
> Below are the lines that I typed in the R window and let me know if anyone
> knows how to resolve this.
>
> Var=read.csv("03apr10ab_corr_matrix_in_overlaps.csv",header=F)
> colnames(Var)=c("D Prime","T statistics")
>
>          D Prime    T statistics
> 1    1.7234e-01     4.926800
> 2    1.4399e-01     2.892000
> 3    1.4626e-01     2.642800
> 4    3.5147e-02     1.112400
> 5    5.8957e-02     2.723700
>
>
> rcorr(Var, type="pearson")

Untested (because I'm still without respectable internet after a move)
I believe rcorr would rather have a matrix than a data.frame(), which
is what read.csv produces, so try

Var <- as.matrix(Var)

or

rcorr(as.matrix(Var), type = "pearson")

>
> Error in storage.mode(x) <- if (.R.) "double" else "single" :
>   (list) object cannot be coerced to type 'double'

This suggests that the input to rcorr is being converted to a double,
which isn't a valid storage.mode change for a list (= data frame).

Cheers,
M

>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[Bert Gunter]

Have you read (relevant sections) of "An Introduction to R"  to gain
some basic understanding of how R works? If not, please do so before
further posting.

Briefly, Var is a data frame and rcorr wants a matrix.

-- Bert

On Wed, Sep 12, 2012 at 8:04 AM, Jason Love <[hidden email]> wrote:

> Hello,
> I'd like to test a significance of two variables in their correlation using
> rcorr, which gave me an error of format incompatibility.
> Below are the lines that I typed in the R window and let me know if anyone
> knows how to resolve this.
>
> Var=read.csv("03apr10ab_corr_matrix_in_overlaps.csv",header=F)
> colnames(Var)=c("D Prime","T statistics")
>
>          D Prime    T statistics
> 1    1.7234e-01     4.926800
> 2    1.4399e-01     2.892000
> 3    1.4626e-01     2.642800
> 4    3.5147e-02     1.112400
> 5    5.8957e-02     2.723700
>
>
> rcorr(Var, type="pearson")
>
> Error in storage.mode(x) <- if (.R.) "double" else "single" :
>   (list) object cannot be coerced to type 'double'
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

--

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: [phone]
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

______________________________________________
[hidden email] mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[Rui Barradas]

Hello,

The input must be a matrix, not a list (or its special case data.frame).

Var <- read.table(text="
   D.Prime    T.statistics
1    1.7234e-01     4.926800
2    1.4399e-01     2.892000
3    1.4626e-01     2.642800
4    3.5147e-02     1.112400
5    5.8957e-02     2.723700
", header=TRUE)

# library(Hmisc)
rc <- rcorr(as.matrix(Var), type="pearson")
# from recommended package stats
ct <- cor.test(Var$D.Prime, Var$T.statistics, method = "pearson")

rc$P
                D.Prime T.statistics
D.Prime             NA    0.1101842
T.statistics 0.1101842           NA

ct$p.value
[1] 0.1101842

To the op: you should say which library you are using. Even if Hmisc is
a very popular one.

Hope this helps,

Rui Barradas


Em 12-09-2012 16:10, R. Michael Weylandt escreveu:

> On Wed, Sep 12, 2012 at 4:04 PM, Jason Love <[hidden email]> wrote:
>> Hello,
>> I'd like to test a significance of two variables in their correlation using
>> rcorr, which gave me an error of format incompatibility.
>> Below are the lines that I typed in the R window and let me know if anyone
>> knows how to resolve this.
>>
>> Var=read.csv("03apr10ab_corr_matrix_in_overlaps.csv",header=F)
>> colnames(Var)=c("D Prime","T statistics")
>>
>>           D Prime    T statistics
>> 1    1.7234e-01     4.926800
>> 2    1.4399e-01     2.892000
>> 3    1.4626e-01     2.642800
>> 4    3.5147e-02     1.112400
>> 5    5.8957e-02     2.723700
>>
>>
>> rcorr(Var, type="pearson")
> Untested (because I'm still without respectable internet after a move)
> I believe rcorr would rather have a matrix than a data.frame(), which
> is what read.csv produces, so try
>
> Var <- as.matrix(Var)
>
> or
>
> rcorr(as.matrix(Var), type = "pearson")
>
>> Error in storage.mode(x) <- if (.R.) "double" else "single" :
>>    (list) object cannot be coerced to type 'double'
> This suggests that the input to rcorr is being converted to a double,
> which isn't a valid storage.mode change for a list (= data frame).
>
> Cheers,
> M
>
>>          [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[Jason Love]

thanks all for the prompt answer.
Yes, I need to go through the R tutorial rather than learning a snippet of
codes from googling.


On Wed, Sep 12, 2012 at 11:32 AM, Rui Barradas <[hidden email]> wrote:

> Hello,
>
> The input must be a matrix, not a list (or its special case data.frame).
>
> Var <- read.table(text="
>   D.Prime    T.statistics
>
> 1    1.7234e-01     4.926800
> 2    1.4399e-01     2.892000
> 3    1.4626e-01     2.642800
> 4    3.5147e-02     1.112400
> 5    5.8957e-02     2.723700
> ", header=TRUE)
>
> # library(Hmisc)
> rc <- rcorr(as.matrix(Var), type="pearson")
> # from recommended package stats
> ct <- cor.test(Var$D.Prime, Var$T.statistics, method = "pearson")
>
> rc$P
>                D.Prime T.statistics
> D.Prime             NA    0.1101842
> T.statistics 0.1101842           NA
>
> ct$p.value
> [1] 0.1101842
>
> To the op: you should say which library you are using. Even if Hmisc is a
> very popular one.
>
> Hope this helps,
>
> Rui Barradas
>
>
> Em 12-09-2012 16:10, R. Michael Weylandt escreveu:
>
>  On Wed, Sep 12, 2012 at 4:04 PM, Jason Love <[hidden email]>
>> wrote:
>>
>>> Hello,
>>> I'd like to test a significance of two variables in their correlation
>>> using
>>> rcorr, which gave me an error of format incompatibility.
>>> Below are the lines that I typed in the R window and let me know if
>>> anyone
>>> knows how to resolve this.
>>>
>>> Var=read.csv("03apr10ab_corr_**matrix_in_overlaps.csv",**header=F)
>>> colnames(Var)=c("D Prime","T statistics")
>>>
>>>           D Prime    T statistics
>>> 1    1.7234e-01     4.926800
>>> 2    1.4399e-01     2.892000
>>> 3    1.4626e-01     2.642800
>>> 4    3.5147e-02     1.112400
>>> 5    5.8957e-02     2.723700
>>>
>>>
>>> rcorr(Var, type="pearson")
>>>
>> Untested (because I'm still without respectable internet after a move)
>> I believe rcorr would rather have a matrix than a data.frame(), which
>> is what read.csv produces, so try
>>
>> Var <- as.matrix(Var)
>>
>> or
>>
>> rcorr(as.matrix(Var), type = "pearson")
>>
>>  Error in storage.mode(x) <- if (.R.) "double" else "single" :
>>>    (list) object cannot be coerced to type 'double'
>>>
>> This suggests that the input to rcorr is being converted to a double,
>> which isn't a valid storage.mode change for a list (= data frame).
>>
>> Cheers,
>> M
>>
>>           [[alternative HTML version deleted]]
>>>
>>> ______________________________**________________
>>> [hidden email] mailing list
>>> https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help>
>>> PLEASE do read the posting guide http://www.R-project.org/**
>>> posting-guide.html <http://www.R-project.org/posting-guide.html>
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>> ______________________________**________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help>
>> PLEASE do read the posting guide http://www.R-project.org/**
>> posting-guide.html <http://www.R-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.