[ftorri]

Actually I noticed that my 'gene' column has a '-' all the way.
I think I am missing the gene short name.
Fed

[rboettcher]

try to use unlist() before using as.vector()

[ftorri]

Thanks for your reply!
I tried, but still it is not a vector:

> myIDs<-read.table("Ids_test.txt")
> unlist()
Error in unlist() : argument "x" is missing, with no default
> unlist(myIDs)
V11 V12 V13 V14 V15 V16 V17 V18 V19 V110 V111 V112 V113 V114 V115 V116 V117 V118 V119
DUSP4 KLF4 RALGAPA1 PCDH11X PTCH1 RAB3IP PALM2 LMLN CDK12 PIP5K1A CSNK1G3 ARSA AKAP2 RNF182 TP73-AS1 RXFP1
{...}
> myIDs<-read.table("Ids_test.txt")
> is.vector(myIDs)
[1] FALSE

Federica

[billstevens]

Hey guys,

Quick question. When I use csScatter following the Nature Protocols paper, it takes a while (3-5minutes) for the image to load. Is there a way to output the image to a file and not have it load up right then, thereby saving time?

[aslihan]

I have same problem like starr and fed.


myIDs<-read.table("gene_name.txt")

It works.There are 2 columns first: number 2nd column: gene_short_name

myGenes<-getGenes(cuff_data,myIDs)
heat<-csHeatmap(myGenes)

ONLY GIVES HEATMAP FOR FIRST ONE GENE!
I tried what you said.

> myIDs<-read.table("gene_name.txt")
> myIDs<-as.vector(myIDs$v1)
> myGenes<-getGenes(cuff_data,myIDs)
Error in sqliteExecStatement(conn, statement, ...) :
RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)


How can I solve problem ?

Thanks a lot.

[ftorri]

Hi, Loyal helped me out in solving this issue.

You have to use:
myIDs<-as.vector(myIDs$V1) with a upper case v.

And then check:
is.vector(myIDs)

It should be true this time.

Fed

[ftorri]

Hi all, does anyone of you know how I can install the developmental version of cummerbund? I am not able to use a lot of utilities with the one I have. I followed the instruction, but still I get the stable version:

> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.4.7, ?biocLite for help
> biocLite("cummeRbund")

thanks,

Fed

[lgoff]

Hi guys,
when you read in IDs using read.table, it creates a data.frame. you must point to the first column and from that create a vector:


myIDs<-read.table("genes_ids.txt")

myIDs<-myIDs[,1] # Will create a vector of the first column values or myIDs$V1 unless you have column headers and then you can use the name of the column instead of V1 (V1 is R's default value for the first column of a data.frame that doesn't have column names. It must be capitalized 'V1')

I recommend that you make sure myIDs is a vector and that it contains all of the IDs you are interested before using it for getGenes...

Cheers,
Loyal

[lgoff]

Hi Fed...
To use the biocLite() installer, you must be running the development version of R (2.16.0). Otherwise, you can download the development version from the cummeRbund website:

http://compbio.mit.edu/cummeRbund/

And then install it from the command line as follows:

R CMD INSTALL cummeRbund_1.99.2.tgz

You may have to install a few additional dependancies to get it working correctly.

Cheers,
Loyal

[scor]

cuff gene set - cummeRbund

Hi all
I am trying to create a cuff gene set (for use with cummerbund) from a list of gene names. I have read the gene names in as a vector. This step seems fine and I have confirmed the vector with 'is.vector'. I do not have gene_ids. When I use the getGenes function on the names vector I do not get a gene set.
I get "CuffGeneSet instance for genes character(0)"

It seems to me that you probably need the list of gene_ids and it is not sufficient to only have a list of gene names.
If anyone can help with advice on how to create a geneset without having a list of gene_ids I would be grateful.

[scor]

cuff gene set - cummeRbund

My apologies - the problem was that my gene names were in lower case. I just needed to change the names to upper case and I have been able to create a gene set.

[vyellapa]

I was going through the CummerBund manual and things were smooth until I hit this error.

> myGenes <- getGenes(cuff, myGeneIds)
Error in sqliteExecStatement(conn, statement, ...) : 
  RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)

I have seen the same error on this post but could not a solution. How can I resolve this error?

[lgoff]

This happens in earlier versions of cummeRbund when a call to the database failed, subsequent calls would generate this error message. You can always re-connect to the database with:

cuff<-readCufflinks()

and this should alleviate the error. I will try to address this better in future versions

Cheers,
Loyal

[vyellapa]

Hi Loyal,
I tried reloading the database and got the same error. If it has anything to do with versioning, I am using R 2.15.1 and cufflinks 2.0.0 with Cummerbund 1.99.

Is there any other way I could try?

> cuff<-readCufflinks()
> myGenes <- getGenes(cuff, myGeneIds)
Getting gene information:
	FPKM
Error in sqliteExecStatement(con, statement, bind.data) : 
  RS-DBI driver: (error in statement: near ")": syntax error)

[IBseq]

HI everyone,
have you ever had something like this when running cummerbund?

> library(cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: ‘fastcluster’

The following object(s) are masked from ‘package:stats’:

hclust

> cuff <- readCufflinks(dir=system.file("myextdata", package="cummeRbund"))
> cuff
CuffSet instance with:
0 samples
0 genes
0 isoforms
0 TSS
0 CDS
0 promoters
0 splicing
0 relCDS

it's all empty!
my cuffdiff outputs come from galaxy, they are in tabular format..

cheers
ib