rcorr error in R stat

3 messages · Rui Barradas, Chaitanya Ganne

Original

1

3

Rui Barradas

Thu, Sep 21, 2017 9:56 AM #

Hello,

Please keep this on the list, always cc r-help.
One of the files in your attachment is empty:

y <- read.csv(file.choose("GT.csv"))
Error in read.table(file = file, header = header, sep = sep, quote = quote,? :
? no lines available in input

Rui Barradas
?

Citando Chaitanya Ganne <Chaitanya.Ganne at jefferson.edu>:

Thank you so much for your input.

I am relatively new to R and I don't understand this "read.csv  
returns data.frames". Sorry.

This however did not work. "unlist(x) and unlist(y)". I got a series  
of 43 warnings:

Warning messages:
1: In doTryCatch(return(expr), name, parentenv, handler) :
? "method" is not a graphical parameter
2: In doTryCatch(return(expr), name, parentenv, handler) :
? "method" is not a graphical parameter
.
.
.
.
.

? "method" is not a graphical parameter
42: In doTryCatch(return(expr), name, parentenv, handler) :
? "method" is not a graphical parameter
43: In cbind(x, y) :
? number of rows of result is not a multiple of vector length (arg 2)
?
Would it help if I send the two csv files to you? I'd really  
appreciate your help.

Thanking you
?

-------------------------
FROM: ruipbarradas at sapo.pt <ruipbarradas at sapo.pt>
SENT: Wednesday, September 20, 2017 5:21:04 PM
TO: Chaitanya Ganne
SUBJECT: Re: rcorr error in R stat

Hello,

Maybe I'm completely off, but read.csv returns data.frames, which  
are lists with a dim attribute.
Instead of as.vector try unlist(x) and unlist(y).

Note that if 'df' is a data.frame, class(as.vector(df)) returns "data.frame".

Hope this helps,

Rui Barradas
?

Citando Chaitanya Ganne <Chaitanya.Ganne at jefferson.edu>:

Good afternoon,?

I have two variables x and y. I am trying to run a correlation  
between them as vectors.?
x <- read.csv(file.choose(NPA.csv))
y <- read.csv(file.choose(GT.csv))
res <- cor(as.vector(x), as.vector(y))
round(res, 2)
install.packages("Hmisc")
library(Hmisc)
res2 <- rcorr(as.vector(x), as.vector(y))
res2 <- rcorr(as.vector(x), as.vector(y))
Error in storage.mode(x) <- "double" :?
?(list) object cannot be coerced to type 'double'
?
---------------------------------------------------

In fact I find this is something to do with the way the matrices  
are being considered for rcorr to be different from the way the  
matrices are being considered for 'cor'. The cor function gave me  
this output as mentioned below. However I am using the rcorr  
function to build the correlplots later on.
? ? ? ? ? ?


  BC_11L_parstriangularis_1 	BC_12L_rostralmiddlefrontal_2  
	BC_20L_fusiform_4 	BC_21L_inferiortemporal_3  
	BC_23L_middletemporal_1 	vw_12L_rostralmiddlefrontal_2  
	vw_19L_inferiorparietal_1
  CVLT_T4 	-0.23 	0.13 	-0.01 	-0.24 	-0.14 	0.02 	0.06
  CVLT_T5 	-0.28 	0.12 	0.04 	-0.25 	-0.19 	0.15 	0.11
  CVLT_Total 	-0.25 	0.07 	0.13 	-0.25 	-0.22 	0.05 	-0.05
  CVLT_LDF 	-0.16 	0.04 	0.16 	-0.23 	-0.32 	0.16 	0.01
  CVLT_RoF 	-0.12 	0.02 	0.06 	-0.04 	-0.14 	0.16 	-0.06
  CVLT_TDR 	-0.11 	0.1 	0.13 	-0.24 	-0.25 	0.25 	-0.06
  LM_I 	-0.46 	-0.19 	-0.11 	-0.06 	-0.24 	-0.01 	0.1
  LM_II 	-0.35 	0.06 	0.05 	-0.11 	-0.31 	0.22 	0.05
  p_REC 	-0.12 	-0.27 	0.36 	-0.19 	-0.09 	-0.17 	-0.21
  TF 	-0.01 	-0.01 	-0.21 	-0.2 	-0.27 	-0.07 	0.06

?
Please help.

/DR. GANNE CHAITANYA MD, PHD/

/PDF?//NEUROLOGY/

/TJU,?//PHILADELPHIA, 19107, PA/


  The information contained in this transmission contains  
privileged and confidential information. It is intended only for  
the use of the person named above. If you are not the intended  
recipient, you are hereby notified that any review, dissemination,  
distribution or duplication of this communication is strictly  
prohibited. If you are not the intended recipient, please contact  
the sender by reply email and destroy all copies of the original  
message.

_CAUTION_: Intended recipients should NOT use email communication  
for emergent or urgent health care matters.

Rui Barradas

Thu, Sep 21, 2017 10:21 AM #

Hello,

Also, the other file, NPA.csv, is not in tabular form. Can you please  
reformat it?

Rui Barradas


Citando ruipbarradas at sapo.pt:

Hello,

Please keep this on the list, always cc r-help.
One of the files in your attachment is empty:

y <- read.csv(file.choose("GT.csv"))
Error in read.table(file = file, header = header, sep = sep, quote =  
quote,? :
? no lines available in input

Rui Barradas
?

Citando Chaitanya Ganne <Chaitanya.Ganne at jefferson.edu>:

Thank you so much for your input.

I am relatively new to R and I don't understand this "read.csv
returns data.frames". Sorry.

This however did not work. "unlist(x) and unlist(y)". I got a series
of 43 warnings:

Warning messages:
1: In doTryCatch(return(expr), name, parentenv, handler) :
? "method" is not a graphical parameter
2: In doTryCatch(return(expr), name, parentenv, handler) :
? "method" is not a graphical parameter
.
.
.
.
.

? "method" is not a graphical parameter
42: In doTryCatch(return(expr), name, parentenv, handler) :
? "method" is not a graphical parameter
43: In cbind(x, y) :
? number of rows of result is not a multiple of vector length (arg 2)
?
Would it help if I send the two csv files to you? I'd really
appreciate your help.

Thanking you
?

-------------------------
FROM: ruipbarradas at sapo.pt <ruipbarradas at sapo.pt>
SENT: Wednesday, September 20, 2017 5:21:04 PM
TO: Chaitanya Ganne
SUBJECT: Re: rcorr error in R stat

Hello,

Maybe I'm completely off, but read.csv returns data.frames, which
are lists with a dim attribute.
Instead of as.vector try unlist(x) and unlist(y).

Note that if 'df' is a data.frame, class(as.vector(df)) returns  
"data.frame".

Hope this helps,

Rui Barradas
?

Citando Chaitanya Ganne <Chaitanya.Ganne at jefferson.edu>:

Good afternoon,?

I have two variables x and y. I am trying to run a correlation
between them as vectors.?
x <- read.csv(file.choose(NPA.csv))
y <- read.csv(file.choose(GT.csv))
res <- cor(as.vector(x), as.vector(y))
round(res, 2)
install.packages("Hmisc")
library(Hmisc)
res2 <- rcorr(as.vector(x), as.vector(y))
res2 <- rcorr(as.vector(x), as.vector(y))
Error in storage.mode(x) <- "double" :?
?(list) object cannot be coerced to type 'double'
?
---------------------------------------------------

In fact I find this is something to do with the way the matrices
are being considered for rcorr to be different from the way the
matrices are being considered for 'cor'. The cor function gave me
this output as mentioned below. However I am using the rcorr
function to build the correlplots later on.
? ? ? ? ? ?


  BC_11L_parstriangularis_1 	BC_12L_rostralmiddlefrontal_2
	BC_20L_fusiform_4 	BC_21L_inferiortemporal_3
	BC_23L_middletemporal_1 	vw_12L_rostralmiddlefrontal_2
	vw_19L_inferiorparietal_1
  CVLT_T4 	-0.23 	0.13 	-0.01 	-0.24 	-0.14 	0.02 	0.06
  CVLT_T5 	-0.28 	0.12 	0.04 	-0.25 	-0.19 	0.15 	0.11
  CVLT_Total 	-0.25 	0.07 	0.13 	-0.25 	-0.22 	0.05 	-0.05
  CVLT_LDF 	-0.16 	0.04 	0.16 	-0.23 	-0.32 	0.16 	0.01
  CVLT_RoF 	-0.12 	0.02 	0.06 	-0.04 	-0.14 	0.16 	-0.06
  CVLT_TDR 	-0.11 	0.1 	0.13 	-0.24 	-0.25 	0.25 	-0.06
  LM_I 	-0.46 	-0.19 	-0.11 	-0.06 	-0.24 	-0.01 	0.1
  LM_II 	-0.35 	0.06 	0.05 	-0.11 	-0.31 	0.22 	0.05
  p_REC 	-0.12 	-0.27 	0.36 	-0.19 	-0.09 	-0.17 	-0.21
  TF 	-0.01 	-0.01 	-0.21 	-0.2 	-0.27 	-0.07 	0.06

?
Please help.

/DR. GANNE CHAITANYA MD, PHD/

/PDF?//NEUROLOGY/

/TJU,?//PHILADELPHIA, 19107, PA/


  The information contained in this transmission contains
privileged and confidential information. It is intended only for
the use of the person named above. If you are not the intended
recipient, you are hereby notified that any review, dissemination,
distribution or duplication of this communication is strictly
prohibited. If you are not the intended recipient, please contact
the sender by reply email and destroy all copies of the original
message.

_CAUTION_: Intended recipients should NOT use email communication
for emergent or urgent health care matters.

?

	[[alternative HTML version deleted]]

______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.

Chaitanya Ganne

Fri, Sep 22, 2017 8:06 AM #

My apologies for the late reply. I had scans after I last messaged you yesterday.


Please find attached the ms-dos CSV file which I prepared using microsoft excel. there should be GT1.csv and NPA1.csv.


Thanking you

From: ruipbarradas at sapo.pt <ruipbarradas at sapo.pt>
Sent: Thursday, September 21, 2017 1:21:22 PM
To: Chaitanya Ganne; r-help
Subject: Re: [R] rcorr error in R stat

Hello,

Also, the other file, NPA.csv, is not in tabular form. Can you please
reformat it?

Rui Barradas


Citando ruipbarradas at sapo.pt:
> Hello,
>
> Please keep this on the list, always cc r-help.
> One of the files in your attachment is empty:
>
> y <- read.csv(file.choose("GT.csv"))
> Error in read.table(file = file, header = header, sep = sep, quote =
> quote,  :
>   no lines available in input
>
> Rui Barradas
>
>
> Citando Chaitanya Ganne <Chaitanya.Ganne at jefferson.edu>:
>
>> Thank you so much for your input.
>>
>> I am relatively new to R and I don't understand this "read.csv
>> returns data.frames". Sorry.
>>
>> This however did not work. "unlist(x) and unlist(y)". I got a series
>> of 43 warnings:
>>
>> Warning messages:
>> 1: In doTryCatch(return(expr), name, parentenv, handler) :
>>   "method" is not a graphical parameter
>> 2: In doTryCatch(return(expr), name, parentenv, handler) :
>>   "method" is not a graphical parameter
>> .
>> .
>> .
>> .
>> .
>>
>>   "method" is not a graphical parameter
>> 42: In doTryCatch(return(expr), name, parentenv, handler) :
>>   "method" is not a graphical parameter
>> 43: In cbind(x, y) :
>>   number of rows of result is not a multiple of vector length (arg 2)
>>
>> Would it help if I send the two csv files to you? I'd really
>> appreciate your help.
>>
>> Thanking you
>>
>>
>> -------------------------
>> FROM: ruipbarradas at sapo.pt <ruipbarradas at sapo.pt>
>> SENT: Wednesday, September 20, 2017 5:21:04 PM
>> TO: Chaitanya Ganne
>> SUBJECT: Re: rcorr error in R stat
>>
>> Hello,
>>
>> Maybe I'm completely off, but read.csv returns data.frames, which
>> are lists with a dim attribute.
>> Instead of as.vector try unlist(x) and unlist(y).
>>
>> Note that if 'df' is a data.frame, class(as.vector(df)) returns
>> "data.frame".
>>
>> Hope this helps,
>>
>> Rui Barradas
>>
>>
>> Citando Chaitanya Ganne <Chaitanya.Ganne at jefferson.edu>:
>>
>>> Good afternoon,
>>>
>>> I have two variables x and y. I am trying to run a correlation
>>> between them as vectors.
>>> x <- read.csv(file.choose(NPA.csv))
>>> y <- read.csv(file.choose(GT.csv))
>>> res <- cor(as.vector(x), as.vector(y))
>>> round(res, 2)
>>> install.packages("Hmisc")
>>> library(Hmisc)
>>> res2 <- rcorr(as.vector(x), as.vector(y))
>>> res2 <- rcorr(as.vector(x), as.vector(y))
>>> Error in storage.mode(x) <- "double" :
>>>  (list) object cannot be coerced to type 'double'
>>>
>>> ---------------------------------------------------
>>>
>>> In fact I find this is something to do with the way the matrices
>>> are being considered for rcorr to be different from the way the
>>> matrices are being considered for 'cor'. The cor function gave me
>>> this output as mentioned below. However I am using the rcorr
>>> function to build the correlplots later on.
>>>
>>>
>>>
>>>   BC_11L_parstriangularis_1  BC_12L_rostralmiddlefrontal_2
>>>      BC_20L_fusiform_4        BC_21L_inferiortemporal_3
>>>      BC_23L_middletemporal_1  vw_12L_rostralmiddlefrontal_2
>>>      vw_19L_inferiorparietal_1
>>>   CVLT_T4    -0.23    0.13     -0.01    -0.24    -0.14    0.02     0.06
>>>   CVLT_T5    -0.28    0.12     0.04     -0.25    -0.19    0.15     0.11
>>>   CVLT_Total         -0.25    0.07     0.13     -0.25    -0.22    0.05     -0.05
>>>   CVLT_LDF   -0.16    0.04     0.16     -0.23    -0.32    0.16     0.01
>>>   CVLT_RoF   -0.12    0.02     0.06     -0.04    -0.14    0.16     -0.06
>>>   CVLT_TDR   -0.11    0.1      0.13     -0.24    -0.25    0.25     -0.06
>>>   LM_I       -0.46    -0.19    -0.11    -0.06    -0.24    -0.01    0.1
>>>   LM_II      -0.35    0.06     0.05     -0.11    -0.31    0.22     0.05
>>>   p_REC      -0.12    -0.27    0.36     -0.19    -0.09    -0.17    -0.21
>>>   TF         -0.01    -0.01    -0.21    -0.2     -0.27    -0.07    0.06
>>>
>>>
>>> Please help.
>>>
>>> /DR. GANNE CHAITANYA MD, PHD/
>>>
>>> /PDF //NEUROLOGY/
>>>
>>> /TJU, //PHILADELPHIA, 19107, PA/
>>>
>>>
>>>   The information contained in this transmission contains
>>> privileged and confidential information. It is intended only for
>>> the use of the person named above. If you are not the intended
>>> recipient, you are hereby notified that any review, dissemination,
>>> distribution or duplication of this communication is strictly
>>> prohibited. If you are not the intended recipient, please contact
>>> the sender by reply email and destroy all copies of the original
>>> message.
>>>
>>> _CAUTION_: Intended recipients should NOT use email communication
>>> for emergent or urgent health care matters.
>>
>>
>
>
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-help&data=02%7C01%7CChaitanya.Ganne%40jefferson.edu%7C2294ae18fd7e4a3b9fcd08d501153840%7C55a89906c710436bbc444c590cb67c4a%7C0%7C0%7C636416113005878432&sdata=QZ6qfoYeF2NGwDcQ2ASnZQCAI0OnYDQ%2FhBBQzhN7fJQ%3D&reserved=0
> PLEASE do read the posting guide https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.R-project.org%2Fposting-guide.html&data=02%7C01%7CChaitanya.Ganne%40jefferson.edu%7C2294ae18fd7e4a3b9fcd08d501153840%7C55a89906c710436bbc444c590cb67c4a%7C0%7C0%7C636416113005878432&sdata=1fr2Lpgsa7T0Y%2BjD%2FO35d%2FezFGKMdzdO0WE4RTNG7Po%3D&reserved=0
> and provide commented, minimal, self-contained, reproducible code.




The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.

CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.