Hi Keep your answers to R help (others can help you too)
Need Help to solve an Error in R
3 messages · PIKAL Petr, David Winsemius, Jim Lemon
On Apr 15, 2016, at 6:07 AM, PIKAL Petr <petr.pikal at precheza.cz> wrote: 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.
To Jyoti; The first line of code in the help file fails with a message:
make.gal.env(galname='galenv', gal.path='Exiqon')
Error in make.gal.env(galname = "galenv", gal.path = "Exiqon") : Cannot find GAL file. The package documentation mentions a file named GSE20122_RAW.tar at (http://www.ncbi.nlm.nih.gov/geo/) You can find this at an NIH website: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20122 . Status Public on Feb 02, 2010 Title Vitamin D and microRNA Expression The file is linked to at the bottom of that document. It's 87.7 Mb and only expands to a directory slightly large, because the contents are all gzipped. The server is reasonably fast so download only takes a few minutes. The documentation then describes the process for extracting text files. The first file is named GSM503404_Hy3_Exiqon_14114404_S01_Cropped.txt.gz and each of the 108 items are slightly over 900 KB. The unlabeled appendix at the end of the vignette has 24 file names at least some of which are in the 108 items. You are given directions about how to store these names in a text file. The package vignette appears to be a "work in progress" because references to figures and appendices are often to "??". It does describe a process for constructing a directory that can be used with package functions, but there are no code segments to copy, either in the vignette or this the help page link to "R code". You are much more likely to find someone who knows anything further about this package at the Bioconductor help page. (It is a Bioconductor package after all.) They have a spiffy new Q&A interface that reminds me of StackOverflow. I suspect a lot of newbies find it easier to use than the text based mailing list: https://support.bioconductor.org/
David. > 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]] >> >> ______________________________________________ >> R-help at r-project.org<mailto: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. > > ________________________________ > Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m. > Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu. > Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. > Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i zpo?d?n?m p?enosu e-mailu. > > V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: > - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. > - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce s dodatkem ?i odchylkou. > - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. > - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich existence je adres?tovi ?i osob? j?m zastoupen? zn?m?. > > 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. > > In case that this e-mail forms part of business dealings: > - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning. > - 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. > > > > -- > Regards > > Jyoti Sharma > Junior Research Fellow > University of Hyderabad > India > > ________________________________ > Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m. > Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu. > Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. > Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i zpo?d?n?m p?enosu e-mailu. > > V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: > - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. > - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce s dodatkem ?i odchylkou. > - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. > - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich existence je adres?tovi ?i osob? j?m zastoupen? zn?m?. > > 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. > > In case that this e-mail forms part of business dealings: > - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning. > - 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. > > [[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. David Winsemius Alameda, CA, USA
1 day later
Hi Jyoti,
From what you and others have written I am going to guess that you are
using Windows, that Windows has hidden the extension on the file you are trying to read, and the filename is actually: galenv.gal I may be wrong, but this problem has beset others before you. Jim
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 ??