[BioC] Problems in running easyRNASeq

[Jeya [guest]]

I am interested in analysing the differential expression of the transcriptome of A.flavus grown at two different condition using easyRNASeq and DEGSeq.  I have the raw reads in fastq format for the expt.  I had mapped these reads to the reference genome sequence using bowtie and the output bam file was given as input to easyRNASeq.  It gave the error ".doBasicCount(obj) : The genomicAnnotation slot is empty".  When I gave the tophat generated bam file (along with the bai), I get the same error.  How to overcome this problem.  

 -- output of sessionInfo(): 

> easyRNASeq(filesDirectory=("/home/Dharmalingam/Documents/Bioconductor/eg/Aflavus/rnaseq/"), organism="Aflavus", readLength=100L, annotationMethod="gtf", annotationFile="Aspergillus_flavus.JCVI-afl1-v2.0.16 (1).gtf", count="exons", filenames=c("30accepted_hits.bam", "37accepted_hits.bam"))
Checking arguments... 
Fetching annotations... 
Read 103401 records
Summarizing counts... 
Processing 30accepted_hits.bam 
Error in .doBasicCount(obj) : The genomicAnnotation slot is empty
In addition: Warning messages:
1: In easyRNASeq(filesDirectory = ("/home/Dharmalingam/Documents/Bioconductor/eg/Aflavus/rnaseq/"),  :
  Your organism has no mapping defined to perform the validity check for the UCSC compliance of the chromosome name.
Defined organism's mapping can be listed using the 'knownOrganisms' function.
To benefit from the validity check, you can provide a 'chr.map' to your 'easyRNASeq' function call.
As you did not do so, 'validity.check' is turned off
2: In .Method(..., deparse.level = deparse.level) :
  number of columns of result is not a multiple of vector length (arg 256)
3: In easyRNASeq(filesDirectory = ("/home/Dharmalingam/Documents/Bioconductor/eg/Aflavus/rnaseq/"),  :
  There are 59 features/exons defined in your annotation that overlap! This implies that some reads will be counted more than once! Is that really what you want?


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