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Old 12-02-2015, 09:03 AM   #1
szy0931
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Default cummeRbund cannot read cuffdiff results

I ran cuffdiff on Galaxy and downloaded the resulting .tabular files.
However, cummeRbund on my computer (windows 10, R environment) cannot open the .tabular files.
How to change the tabular format to a format that can bed opened by cummeRbund?
Thank you very much!
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Old 12-02-2015, 09:27 AM   #2
blancha
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Have you tried the function readCufflinks?
If not, that would be your first step.
If you have already tried, what was the error message, and what is your session info?
sessionInfo()
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Old 12-02-2015, 02:01 PM   #3
szy0931
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Quote:
Originally Posted by blancha View Post
Have you tried the function readCufflinks?
If not, that would be your first step.
If you have already tried, what was the error message, and what is your session info?
sessionInfo()

I just ran like this

> setwd("C:/Users/szy0931/Desktop/A")
> library(cummeRbund)
> cuff=readCufflinks(dbFile="cuffData.db",
+ splicing="581",
+ promoters="582",
+ CDSoverloading="583",
+ CDSFPKMdifferential="584",
+ CDSFPKMtracking="585",
+ TSSgroupsdifferential="586",
+ TSSgroupsFPKMtracking="587",
+ genedifferential="588",
+ geneFPKM="589",
+ transcriptdifferential="590",
+ transcriptFPKM="591",
+ rebuild=T)

Here:
581-591 are the names I renamed the tabular files I downloaded from galaxy
581 is: Galaxy581-[Cuffdiff_on_data_519,_data_514,_and_others__splicing_differential_expression_testing]
582 is: Galaxy582-[Cuffdiff_on_data_519,_data_514,_and_others__promoters_differential_expression_testing]
583 is:Galaxy583-[Cuffdiff_on_data_519,_data_514,_and_others__CDS_overloading_diffential_expression_testing]
584 is:Galaxy584-[Cuffdiff_on_data_519,_data_514,_and_others__CDS_FPKM_differential_expression_testing]
585 is: Galaxy585-[Cuffdiff_on_data_519,_data_514,_and_others__CDS_FPKM_tracking]
586 is: Galaxy586-[Cuffdiff_on_data_519,_data_514,_and_others__TSS_groups_differential_expression_testing]
587 is: Galaxy587-[Cuffdiff_on_data_519,_data_514,_and_others__TSS_groups_FPKM_tracking]
588 is: Galaxy588-[Cuffdiff_on_data_519,_data_514,_and_others__gene_differential_expression_testing]
589 is:Galaxy589-[Cuffdiff_on_data_519,_data_514,_and_others__gene_FPKM_tracking]
590 is: Galaxy590-[Cuffdiff_on_data_519,_data_514,_and_others__transcript_differential_expression_testing]
591 is:Galaxy591-[Cuffdiff_on_data_519,_data_514,_and_others__transcript_FPKM_tracking]

The file "Galaxy592-[Cuffdiff_on_data_519,_data_514,_and_others__cummeRbund_SQLite_database]" was also downloaded.

I got the following:
Creating database C:/Users/szy0931/Desktop/A/cuffData.db
Reading C:/Users/szy0931/Desktop/A/589
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'C:/Users/szy0931/Desktop/A/589': No such file or directory

It looks 589 has some problems.

I then ran
> list.files()
I got this:
[1] "581.tabular" "582.tabular" "583.tabular" "584.tabular" "585.tabular" "586.tabular" "587.tabular" "588.tabular" "589.tabular" "590.tabular" "591.tabular"
[12] "592.sqlite" "cuffData.db"
So, it means 589 is here, right?

I ran sessionInfo()
> sessionInfo()
I got:
Attached Images
File Type: png ????20151202172555.png (36.6 KB, 2 views)

Last edited by szy0931; 12-02-2015 at 02:28 PM.
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Old 12-08-2015, 07:04 AM   #4
szy0931
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Default

figured out. I used run names. I am a totally idiot.
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