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Fix Ace

2017-May-23 17:27 UTC

[R] prcomp: Error in La.svd(x, nu, nv): error code 1 from Lapack routine "dgesdd"

Dear R community,
I have a data matrix (531X314), and would like to apply the prcomp. However, I
got this error Lapack message. I am using R3.2.2.
I googled a bit and found that it might be related to converge issue. ?Just
wonder if there is a way to get around it?
Thank you very much!
Ace 

    On Thursday, December 29, 2016 11:44 AM, Ista Zahn <istazahn at
gmail.com> wrote:
 

 Use coord_fixed()

--Ista

On Thu, Dec 29, 2016 at 9:59 AM, Fix Ace via R-help
<r-help at r-project.org> wrote:>
>
>
>? Hello, there,
> What exactly does "expand" do for this function?
> I followed the examples from the manual to get a plot:
>
> d <- ggplot(subset(diamonds, carat > 1), aes(cut, clarity))
+geom_jitter()
>
> I would like to have all the dots in a square instead of rectangular range.
When I applied d + scale_x_discrete(expand=c(1,1)) and d +
scale_x_discrete(expand=c(1,0)), I got the same plot (different from the
original one though).
> Could anyone help me to figure out how to use this argument?
> Thank you very much!
> Ace
>
>
>
>
>
>? ? ? ? [[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.

   
	[[alternative HTML version deleted]]

Fix Ace

2017-Aug-27 20:25 UTC

head link

[R] help with read.csv() for files with different number of columns

Dear R community,
I have a text file (test.txt) with different number of columns:
0610007P14Rik%%% Tcf19 Gtf2i 0610010O12Rik%%% Ivns1abp Etv6 1100001G20Rik%%% Nmi
1500015O10Rik%%% Foxi1 Ascl3 Sirt3 1700003E16Rik%%% Ascl2 Ifnar2
1700028J19Rik%%% Musk Nfe2l3 1810011O10Rik%%% Ppp1r13b Bpnt1 Cdkn2c Foxc1 Sox10
Smarca2 1810019D21Rik%%% Asb8 1810037I17Rik%%% Zfp612 1810055G02Rik%%% Nkx2-3
Maged1 Runx1 Ugp2 Elk4 Spdef Tcf19 Isl2 Gtf2i Ctnnbl1 Tcea3 Ank2 Zfp612 Creb3l1
Nupr1 3632451O06Rik Creb3l4 Lass6
I wold like to read it into R using
 > test=read.csv("test.txt",sep="\t",header=FALSE)
However, when I check the r object "test", I found that all the rows
have 5 columns:> test?? ? ? ? ? ? ? ? V1? ? ? ? ? ? V2? ? ? V3 ? ? V4? ? ? V51?
0610007P14Rik%%% ? ? ? ? Tcf19 ? Gtf2i? ? ? ? ? ? ? ?2? 0610010O12Rik%%%? ? ?
Ivns1abp? ? Etv6? ? ? ? ? ? ? ?3? 1100001G20Rik%%% ? ? ? ? ? Nmi? ? ? ? ? ? ? ?
? ? ? ?4? 1500015O10Rik%%% ? ? ? ? Foxi1 ? Ascl3? Sirt3 ? ? ? ?5?
1700003E16Rik%%% ? ? ? ? Ascl2? Ifnar2? ? ? ? ? ? ? ?6? 1700028J19Rik%%%? ? ? ?
? Musk? Nfe2l3? ? ? ? ? ? ? ?7? 1810011O10Rik%%%? ? ? Ppp1r13b ? Bpnt1 Cdkn2c ?
Foxc18 ? ? ? ? ? ? Sox10 ? ? ? Smarca2? ? ? ? ? ? ? ? ? ? ? ?9?
1810019D21Rik%%%? ? ? ? ? Asb8? ? ? ? ? ? ? ? ? ? ? ?10 1810037I17Rik%%%? ? ? ?
Zfp612? ? ? ? ? ? ? ? ? ? ? ?11 1810055G02Rik%%%? ? ? ? Nkx2-3? Maged1? Runx1? ?
Ugp212 ? ? ? ? ? ? Elk4 ? ? ? ? Spdef ? Tcf19 ? Isl2 ? Gtf2i13? ? ? ? ? Ctnnbl1
? ? ? ? Tcea3? ? Ank2 Zfp612 Creb3l114? ? ? ? ? ? Nupr1 3632451O06Rik Creb3l4?
Lass6?Basically it breaks some rows into more than one rows. For example, row 7 in the
original record becomes two rows. Looks like the "test" always has 5
columns.?
How does this happen? How should I fix it to make one record into one two in R
object?
Thank you very much!
Ace




 


   
	[[alternative HTML version deleted]]

Bert Gunter

2017-Aug-27 23:04 UTC

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[R] help with read.csv() for files with different number of columns

Email a mess. Too hard for me to decipher, maybe also for others.

If no response, send plain text, as requested by posting guide.

Cheers,
Bert


Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Sun, Aug 27, 2017 at 1:25 PM, Fix Ace via R-help
<r-help at r-project.org> wrote:> Dear R community,
> I have a text file (test.txt) with different number of columns:
> 0610007P14Rik%%% Tcf19 Gtf2i 0610010O12Rik%%% Ivns1abp Etv6
1100001G20Rik%%% Nmi 1500015O10Rik%%% Foxi1 Ascl3 Sirt3 1700003E16Rik%%% Ascl2
Ifnar2 1700028J19Rik%%% Musk Nfe2l3 1810011O10Rik%%% Ppp1r13b Bpnt1 Cdkn2c Foxc1
Sox10 Smarca2 1810019D21Rik%%% Asb8 1810037I17Rik%%% Zfp612 1810055G02Rik%%%
Nkx2-3 Maged1 Runx1 Ugp2 Elk4 Spdef Tcf19 Isl2 Gtf2i Ctnnbl1 Tcea3 Ank2 Zfp612
Creb3l1 Nupr1 3632451O06Rik Creb3l4 Lass6
> I wold like to read it into R using
>  > test=read.csv("test.txt",sep="\t",header=FALSE)
> However, when I check the r object "test", I found that all the
rows have 5 columns:
>> test                 V1            V2      V3     V4      V51 
0610007P14Rik%%%         Tcf19   Gtf2i               2  0610010O12Rik%%%     
Ivns1abp    Etv6               3  1100001G20Rik%%%           Nmi                
4  1500015O10Rik%%%         Foxi1   Ascl3  Sirt3        5  1700003E16Rik%%%     
Ascl2  Ifnar2               6  1700028J19Rik%%%          Musk  Nfe2l3           
7  1810011O10Rik%%%      Ppp1r13b   Bpnt1 Cdkn2c   Foxc18             Sox10     
Smarca2                       9  1810019D21Rik%%%          Asb8                 
10 1810037I17Rik%%%        Zfp612                       11 1810055G02Rik%%%     
Nkx2-3  Maged1  Runx1    Ugp212             Elk4         Spdef   Tcf19   Isl2  
Gtf2i13          Ctnnbl1         Tcea3    Ank2 Zfp612 Creb3l114            Nupr1
3632451O06Rik Creb3l4  Lass6
> Basically it breaks some rows into more than one rows. For example, row 7
in the original record becomes two rows. Looks like the "test" always
has 5 columns.
> How does this happen? How should I fix it to make one record into one two
in R object?
> Thank you very much!
> Ace
>
>
>
>
>
>
>
>
>         [[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.

Jim Lemon

2017-Aug-27 23:25 UTC

head link

[R] help with read.csv() for files with different number of columns

Hi Ace,
As your example seems to have spaces as separators,

testdf<-read.table("test.txt",header=FALSE,fill=TRUE,
col.names=paste("V",1:14,sep=""),stringsAsFactors=FALSE)

By specifying the number of columns with "col.names" and using
"fill=TRUE" you can get a data frame with zero length strings where
values are missing in the input file.

Jim

On Mon, Aug 28, 2017 at 6:25 AM, Fix Ace via R-help
<r-help at r-project.org> wrote:> Dear R community,
> I have a text file (test.txt) with different number of columns:
> 0610007P14Rik%%% Tcf19 Gtf2i 0610010O12Rik%%% Ivns1abp Etv6
1100001G20Rik%%% Nmi 1500015O10Rik%%% Foxi1 Ascl3 Sirt3 1700003E16Rik%%% Ascl2
Ifnar2 1700028J19Rik%%% Musk Nfe2l3 1810011O10Rik%%% Ppp1r13b Bpnt1 Cdkn2c Foxc1
Sox10 Smarca2 1810019D21Rik%%% Asb8 1810037I17Rik%%% Zfp612 1810055G02Rik%%%
Nkx2-3 Maged1 Runx1 Ugp2 Elk4 Spdef Tcf19 Isl2 Gtf2i Ctnnbl1 Tcea3 Ank2 Zfp612
Creb3l1 Nupr1 3632451O06Rik Creb3l4 Lass6
> I wold like to read it into R using
>  > test=read.csv("test.txt",sep="\t",header=FALSE)
> However, when I check the r object "test", I found that all the
rows have 5 columns:
>> test                 V1            V2      V3     V4      V51 
0610007P14Rik%%%         Tcf19   Gtf2i               2  0610010O12Rik%%%     
Ivns1abp    Etv6               3  1100001G20Rik%%%           Nmi                
4  1500015O10Rik%%%         Foxi1   Ascl3  Sirt3        5  1700003E16Rik%%%     
Ascl2  Ifnar2               6  1700028J19Rik%%%          Musk  Nfe2l3           
7  1810011O10Rik%%%      Ppp1r13b   Bpnt1 Cdkn2c   Foxc18             Sox10     
Smarca2                       9  1810019D21Rik%%%          Asb8                 
10 1810037I17Rik%%%        Zfp612                       11 1810055G02Rik%%%     
Nkx2-3  Maged1  Runx1    Ugp212             Elk4         Spdef   Tcf19   Isl2  
Gtf2i13          Ctnnbl1         Tcea3    Ank2 Zfp612 Creb3l114            Nupr1
3632451O06Rik Creb3l4  Lass6
> Basically it breaks some rows into more than one rows. For example, row 7
in the original record becomes two rows. Looks like the "test" always
has 5 columns.
> How does this happen? How should I fix it to make one record into one two
in R object?
> Thank you very much!
> Ace
>
>
>
>
>
>
>
>
>         [[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.

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