Hi,
I've just easyRNAseq before a couple of months ago without problems.
Now I get the following error:
Error in aggregate.data.frame(as.data.frame(x), ...) :
no rows to aggregate
Why????
I've already checked that the chromosome sizes of my alignment genome are identical to the BSgenome.Hspaiens.UCSC.hg19 ones...
Here it goes:
> library(easyRNASeq)
> library(BSgenome.Hsapiens.UCSC.hg19)
> setwd('/home/sylvian/SerumFedStarved/DESeq/')
> bamfiles=dir(getwd(), pattern='*paired_sorted.bam$')
> conditions=c('fed','starved','fed','starved','fed','starved')
> names(conditions)<-c('DRSNpilot1_STARhg19_paired_sorted.bam','DRSNpilot2_STARh g19_paired_sorted.bam','TQ24_STARhg19_paired_sorted.bam','TQ25_STARhg19_paired_s orted.bam','TQ28_STARhg19_paired_sorted.bam','TQ29_STARhg19_paired_sorted.bam')
> rnaseqgenes <- easyRNASeq(filesDirectory=getwd(),
+ organism='Hsapiens',
+ chr.sizes='auto',
+ readLength=100L,
+ annotationMethod='biomaRt',
+ format='bam',
+ count='genes',
+ summarization='geneModels',
+ filenames=bamfiles,
+ conditions=conditions,
+ normalization=TRUE,
+ fitType='local',
+ outputFormat='DESeq',
+ validity.check=TRUE)
Checking arguments...
Fetching annotations...
Computing gene models...
Summarizing counts...
Processing DRSNpilot1_STARhg19_paired_sorted.bam
Error in aggregate.data.frame(as.data.frame(x), ...) :
no rows to aggregate
In addition: Warning messages:
1: Consider using 'synthetic transcripts' as described in the section 7.1 of the vignette instead of the count=genes,summarization=geneModels deprecated paradigm.
2: In easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", chr.sizes = "auto", :
There are 20026 synthetic exons as determined from your annotation that overlap! This implies that some reads will be counted more than once! Is that really what you want?
3: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter, :
You enforce UCSC chromosome conventions, however the provided alignments are not compliant. Correcting it.
4: In min(match(uniqueClasses, classOrder)) :
no non-missing arguments to min; returning Inf
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.28.0
[3] easyRNASeq_1.8.8 ShortRead_1.20.0
[5] Rsamtools_1.14.3 GenomicRanges_1.14.4
[7] DESeq_1.14.0 lattice_0.20-15
[9] locfit_1.5-9.1 Biostrings_2.30.1
[11] XVector_0.2.0 IRanges_1.20.7
[13] edgeR_3.4.2 limma_3.16.7
[15] biomaRt_2.18.0 Biobase_2.22.0
[17] genomeIntervals_1.18.0 BiocGenerics_0.8.0
[19] intervals_0.15.0
loaded via a namespace (and not attached):
[1] annotate_1.40.1 AnnotationDbi_1.24.0 bitops_1.0-6
[4] DBI_0.2-7 genefilter_1.44.0 geneplotter_1.40.0
[7] grid_3.0.1 hwriter_1.3 latticeExtra_0.6-26
[10] LSD_2.5 RColorBrewer_1.0-5 RCurl_1.95-4.1
[13] RSQLite_0.11.4 splines_3.0.1 stats4_3.0.1
[16] survival_2.37-4 XML_3.98-1.1 xtable_1.7-4
[19] zlibbioc_1.6.0
>
>
I have no clue what the problem is. The only thing that changed is that I used to load chr.sizes=as.list(seqlengths(Hsapiens) which now retrieves an error.
Help!
