[R] Need Help to solve an Error in R

[PIKAL Petr]

Hi

Keep your answers to R help (others can help you too)

From the warning message it seems to me possible that function ReadExi needs to write something to the working directory. As I said I am not an expert in this package, but commands from help

R> make.gal.env(galname='galenv', gal.path='Exiqon')
R> ebatch <- ReadExi(galname='galenv', txtfile.path='Exiqon')

are rather different from yours and I am not sure if it matters.

Here I understand that
# The folder 'Exiqon' contains the file 'samplesinfo.txt' and the corresponding raw data files in ImaGene format
## Not run: ebatch <- ReadExi(txtfile.path='Exiqon')
# If the GAL environment has already created by the function make.gal.env
## Not run: ebatch <- ReadExi(galenv='galenv', txtfile.path='Exiqon')

if you already created gal environment you shall use it in ReadExi command.

If you do not understand what environment is I again strongly recommend to read R intro, especially chapter 1 and chapter 7.

Cheers
Petr


From: Jyoti Sharma [mailto:31sharmajittu1991 at gmail.com]
Sent: Friday, April 15, 2016 2:46 PM
To: PIKAL Petr <petr.pikal at precheza.cz>
Subject: Re: [R] Need Help to solve an Error in R

First of all Thank you so much for your reply.

I used this code

library(ExiMiR)
make.gal.env(galname='galenv')

fileRead <- ReadExi(txtfile.path = getwd())

after this the error msg prints -

Read header information
Read C:/Users/Kirti/Documents/working/Exiqon/GSM1302311_0_Exiqon_14173049_S01.txt
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'C:/Users/Kirti/Documents/working/Exiqon/NA': Permission denied


2 txt files, one samplesinfo file and one gal file is already in  C:/Users/Kirti/Documents/working/Exiqon/ directory.

Now I fail to understand where is the problem.



On Fri, Apr 15, 2016 at 6:01 PM, PIKAL Petr <petr.pikal at precheza.cz<mailto:petr.pikal at precheza.cz>> wrote:
Hi

If you recently start with R maybe you shall spend some time with R intro document to understand R basics.

I looked to ExiMiR package and I must say that although I am after 20 years quite familiar with R I have problems to understand what I should do and I would need to study thoroughly how those files I shall read in look like.

Maybe some people who are familiar with ExiMiR package can give you more insight but in any case you shall provide not only error message but also commands you used before those errors.

My guess is that you did not specify name of the file correctly.

Cheers
Petr


> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org<mailto:r-help-bounces at r-project.org>] On Behalf Of Jyoti
> Sharma
> Sent: Friday, April 15, 2016 12:02 PM
> To: r-help at r-project.org<mailto:r-help at r-project.org>
> Subject: [R] Need Help to solve an Error in R
>
> Hello Sir/ma'am,
>
> Greetings for the Day !
>
> I am Jyoti Sharma, from India and recently start working on R. I am new in this
> field and my knowledge is not up to the mark, so if I sound dumb then please
> forgive me.
>
> I tried to read some text file in R so that I can do further analysis on those
> files. All files are MicroRNA dataset and in exiqon format. When I write
> function ReadExi and path of my file gives me error - Error in a file(file, "rt") :
> cannot open the connection.
>
> I put a file in the same directory too, even then also it is not working.
> Can you help me on this issue?? Is there any issue with GAL file or
> samplesinfo.txt file as these are to be there in same folder as described in
> ExiMir package ??
>
> I didn't get this issue. Please help on this matter.
>
> Thanks in advance.
>
>
> --
> *Regards*
>
> *Jyoti Sharma*
> *Junior Research Fellow*
> *University of Hyderabad*
> *India*
>
>       [[alternative HTML version deleted]]
>
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> and provide commented, minimal, self-contained, reproducible code.

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--
Regards

Jyoti Sharma
Junior Research Fellow
University of Hyderabad
India

________________________________
Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům.
Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze svého systému.
Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat.
Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či zpožděním přenosu e-mailu.

V případě, že je tento e-mail součástí obchodního jednání:
- vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu.
- a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce s dodatkem či odchylkou.
- trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným dosažením shody na všech jejích náležitostech.
- odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi či osobě jím zastoupené známá.

This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients.
If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system.
If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner.
The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email.

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- if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation.
- the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects.
- the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the recipient.

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