Problem

[znasim09]

I am new to RNA seq analysis, need help in fixing these problems:

First, when i am trying to readcufflinks commond i get these errors:

> library(cummeRbund)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘packagearallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, as.vector, cbind,
colnames, do.call, duplicated, eval, evalq, Filter, Find,
get, intersect, is.unsorted, lapply, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rep.int, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unlist,
unsplit

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 is masked from ‘package:stats’:

hclust

Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid

Attaching package: ‘cummeRbund’

The following object is masked from ‘package:GenomicRanges’:

promoters

The following object is masked from ‘package:IRanges’:

promoters

The following object is masked from ‘package:BiocGenerics’:

conditions

Warning messages:
1: package ‘RSQLite’ was built under R version 3.2.2
2: package ‘ggplot2’ was built under R version 3.2.2
3: package ‘reshape2’ was built under R version 3.2.2
4: package ‘fastcluster’ was built under R version 3.2.2
5: package ‘rtracklayer’ was built under R version 3.2.2
6: package ‘GenomicRanges’ was built under R version 3.2.2
7: package ‘S4Vectors’ was built under R version 3.2.2
> setwd("C:/Users/Zeeshan/Desktop/cuff23")
> cuff_data<-readCufflinks('/users/Zeeshan/Desktop/cuff23',rebuild = TRUE)
Creating database /users/Zeeshan/Desktop/cuff23/cuffData.db
Reading Run Info File /users/Zeeshan/Desktop/cuff23/run.info
Writing runInfo Table
Reading Read Group Info /users/Zeeshan/Desktop/cuff23/read_groups.info
Writing replicates Table
Reading Var Model Info /users/Zeeshan/Desktop/cuff23/var_model.info
Writing varModel Table
Reading /users/Zeeshan/Desktop/cuff23/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading /users/Zeeshan/Desktop/cuff23/gene_exp.diff
Writing geneExpDiffData table
Reading /users/Zeeshan/Desktop/cuff23/promoters.diff
Writing promoterDiffData table
Reading /users/Zeeshan/Desktop/cuff23/genes.count_tracking
Reshaping geneCount table
Recasting
Writing geneCount table
Reading read group info in /users/Zeeshan/Desktop/cuff23/genes.read_group_tracking
Writing geneReplicateData table
Reading /users/Zeeshan/Desktop/cuff23/isoforms.fpkm_tracking
Checking samples table...
OK!
Writing isoforms table
Reshaping isoformData table
Recasting
Writing isoformData table
Reading /users/Zeeshan/Desktop/cuff23/isoform_exp.diff
Writing isoformExpDiffData table
Reading /users/Zeeshan/Desktop/cuff23/isoforms.count_tracking
Reshaping isoformCount table
Recasting
Writing isoformCount table
Reading read group info in /users/Zeeshan/Desktop/cuff23/isoforms.read_group_tracking
Writing isoformReplicateData table
Reading /users/Zeeshan/Desktop/cuff23/tss_groups.fpkm_tracking
Checking samples table...
OK!
Writing TSS table
Reshaping TSSData table
Recasting
Writing TSSData table
Reading /users/Zeeshan/Desktop/cuff23/tss_group_exp.diff
Writing TSSExpDiffData table
Reading /users/Zeeshan/Desktop/cuff23/splicing.diff
Writing splicingDiffData table
Reading /users/Zeeshan/Desktop/cuff23/tss_groups.count_tracking
Reshaping TSSCount table
Recasting
Writing TSSCount table
Reading read group info in /users/Zeeshan/Desktop/cuff23/tss_groups.read_group_tracking
Writing TSSReplicateData table
Reading /users/Zeeshan/Desktop/cuff23/cds.fpkm_tracking
Checking samples table...
OK!
Writing CDS table
Reshaping CDSData table
Recasting
Writing CDSData table
Reading /users/Zeeshan/Desktop/cuff23/cds_exp.diff
Writing CDSExpDiffData table
Reading /users/Zeeshan/Desktop/cuff23/cds.diff
Writing CDSDiffData table
Reading /users/Zeeshan/Desktop/cuff23/cds.count_tracking
Reshaping CDSCount table
Recasting
Writing CDSCount table
Reading read group info in /users/Zeeshan/Desktop/cuff23/cds.read_group_tracking
Writing CDSReplicateData table
Indexing Tables...
Warning messages:
1: attributes are not identical across measure variables; they will be dropped
2: attributes are not identical across measure variables; they will be dropped
3: attributes are not identical across measure variables; they will be dropped
4: attributes are not identical across measure variables; they will be dropped
5: attributes are not identical across measure variables; they will be dropped
6: attributes are not identical across measure variables; they will be dropped
7: attributes are not identical across measure variables; they will be dropped
8: attributes are not identical across measure variables; they will be dropped

And when I try Gene Feature plots (makeGeneRegionTrack), it gives this error:
> genetrack<-makeGeneRegionTrack(myGene)
Error in `[.data.frame`(features(object), , featCols) :
undefined columns selected

Can anyone help me out ??