Fwd: The EdgeR can not be successfully executed due to no R exectuable file, no package 'edgeR' or no expressed transcripts.

[Tin Nguyen Chi]

---------- Forwarded message ----------
From: Tin Nguyen Chi <tin.ng...@gmail.com>
Date: Tue, Aug 14, 2012 at 6:21 PM
Subject: Re: The EdgeR can not be successfully executed due to no R exectuable file, no package 'edgeR' or no expressed transcripts.
To: James Cai <jame...@genomezoo.net>


Hi,

Is your data big/private? Is it possible that you give me a test file for debug.
If the file is too big or not-shareable, you can make a smaller sample and and rerun it, to see if you can repeat the bug. If yes then you can send me the small sample so I can debug

On Tue, Aug 14, 2012 at 5:53 PM, James Cai <jame...@genomezoo.net> wrote:

Hi Tin,

I tried to run the following R code. I have two samples without any replicates. Is this (d<-raw.data[,2:3];) correct?

===============

library(edgeR)

raw.data<-read.delim("Tran_Expression.xls");

d<-raw.data[,2:3];

rownames(d)<-raw.data[,1];

group<-c(rep('GroupA',1),rep('GroupB',1));

d<-estimateCommonDisp(d);

de.com<-exactTest(d);

write.table(topTags(de.com, n=44396)$table,'output.txt',sep=\"\t\");

===============

I obtained the error message at:

rownames(d)<-raw.data[,1];

Error in `row.names<-.data.frame`(`*tmp*`, value = value) : 

  duplicate 'row.names' are not allowed

In addition: Warning message:

non-unique values when setting 'row.names': ‘chr1’, ‘chr10’, ‘chr11’, ‘chr12’, ‘chr13’, ‘chr14’, ‘chr15’, ‘chr16’, ‘chr17’, ‘chr18’, ‘chr19’, ‘chr2’, ‘chr20’, ‘chr21’, ‘chr22’, ‘chr3’, ‘chr4’, ‘chr5’, ‘chr6’, ‘chr7’, ‘chr8’, ‘chr9’, ‘chrM’, ‘chrX’, ‘chrY’ 

Any thought?

James

On Tue, Aug 14, 2012 at 4:31 PM, Tin Nguyen Chi <tin.ng...@gmail.com> wrote:

Hi,

Yeah please use the data in the ifle to run edgeR and see what happen.
I see a lot of error in the log file, don't know if its from edgeR or from SAMMate. In the worst case I will have to debug it with your data

On Tue, Aug 14, 2012 at 5:25 PM, James Cai <jame...@genomezoo.net> wrote:

Hi Tin,

Do you mean I can use this file Tran_Expression.xls as the input of edegR? Anyway, I attached the file in case you would like to take a look.

James

On Tue, Aug 14, 2012 at 4:22 PM, Tin Nguyen Chi <tin.ng...@gmail.com> wrote:

Hi,

Based on the log file, the transcript file is \\a361-0\C1-2T (backup)\tian\idx\Tran_Expression.xls
Can you check it please?

On Tue, Aug 14, 2012 at 5:15 PM, James Cai <jame...@genomezoo.net> wrote:

Hi Tin,

I had successfully got the edgeR result with example data aSAMMATE that provides. However, when using my own data, I obtained the same error massage as before:

 <ERROR>  The EdgeR can not be successfully executed due to no R exectuable file, no package 'edgeR' or no expressed transcripts.

Would you know why? I attached the log file for your information. 

Could you please let me know where the transcript/read_count file is located? I can use that file as the input and do the analysis in R.

Thanks,

James

On Tue, Aug 14, 2012 at 2:21 PM, Tin Nguyen Chi <tin.ng...@gmail.com> wrote:

You are welcome. If you work with transcript quantification, check out the SASeq in SAMMate. We have its manuscript submitted to Oxford Bioinformatics (under major revision atm), in which we showed that SASeq performs the best compared to existing methods

On Tue, Aug 14, 2012 at 1:23 PM, James Cai <jame...@genomezoo.net> wrote:

Thank you for your quick response.

I solved the problem by specifying C:\Program Files\R\R-2.15.1\bin\x64\Rscript.exe

as I was using the 64-bit R.

Thank for letting me know about the latest version.

Best,

James

On Tue, Aug 14, 2012 at 10:46 AM, Tin Nguyen Chi <tin.ng...@gmail.com> wrote:

Hi,

SAMMate has moved to a new place. Please check out the new website http://asammate.sourceforge.net/
We also have SAMMAte 2.7.2 as the lastest version.

Regarding edgeR, the current SAMMate is able to run with R 2.14.2. Running with a later version of R may result in error. After installing edgeR, please set the path to R script as shown in the attached picture. I have tried it this morning and it works fine for me. If you have any question, please let us know.

Thanks

On Tue, Aug 14, 2012 at 9:57 AM, jamescai <jame...@genomezoo.net> wrote:

I am getting the following error messages:

 

6:47:0  <INFO>  Start detecting differentially expressed genes and isoforms using EdgeR.
6:47:1  <ERROR>  The EdgeR can not be successfully executed due to no R exectuable file, no package 'edgeR' or no expressed transcripts.

 

even though I have installed the R, edgeR and setup the R options in SAMMate 2.6.1 in Windows 7.

 

Any suggestions?

 

Thanks,

James Cai

[Tin Nguyen Chi]

Hi,

I checked the gtf, its a mixture of ENSEMBL and HAVANA. It there anything I should know about this gtf? Is this human sample?

Thanks

On Tue, Aug 14, 2012 at 6:42 PM, James Cai <jame...@genomezoo.net> wrote:

OK. They are big files. Be patient.
James

On Tue, Aug 14, 2012 at 5:41 PM, Tin Nguyen Chi <tin.ng...@gmail.com> wrote:

yes, please send me.

On Tue, Aug 14, 2012 at 6:39 PM, James Cai <jame...@genomezoo.net> wrote:

Hi,

May I send you a link to three files: P1.bam P2.bam and a zipped GTF file?

You should be able to repeat the error message and I am glad that you are willing to help.

[Tin Nguyen Chi]

I'm glad that it works for you.

On Wed, Aug 15, 2012 at 3:56 PM, James Cai <jame...@genomezoo.net> wrote:

It works with replicates.

thank you!

James

On Wed, Aug 15, 2012 at 11:32 AM, Tin Nguyen Chi <tin.ng...@gmail.com> wrote:

Hi,

I use Windows7. How does it perform with more replicates?

On Wed, Aug 15, 2012 at 12:17 PM, James Cai <jame...@genomezoo.net> wrote:

Amazing...I don't know how your computer did it. You used Windows or Mac?

I thought the problem could be due to the lack of replicate. So I copied the p1.bam and make p1_1.bam and p1_2.bam to use them as though there is one replicate.

James 

On Wed, Aug 15, 2012 at 11:11 AM, Tin Nguyen Chi <tin.ng...@gmail.com> wrote:

Hi

SAMMate finished without problem on my computer. Please check the attachments

Thanks

On Tue, Aug 14, 2012 at 7:32 PM, James Cai <jame...@genomezoo.net> wrote:

I downloaded the GTF file from http://www.gencodegenes.org/

If you think that could be the problem, I can try to use Homo_sapiens_Ensembl_GRCh37 for example.

Would you believe that will help?