Question: easyRNASeq error: Error in aggregate.data.frame(as.data.frame(x), ...) : no rows to aggregate
0
gravatar for sylvian
4.7 years ago by
sylvian0
United States
sylvian0 wrote:

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!

 

easyrnaseq • 1.8k views
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by sylvian0
Answer: easyRNASeq error: Error in aggregate.data.frame(as.data.frame(x), ...) : no ro
0
gravatar for sylvian
4.7 years ago by
sylvian0
United States
sylvian0 wrote:

I even now re-headered all my bam files from the original sam - still the same problem :/

 

 

 

ADD COMMENTlink written 4.7 years ago by sylvian0
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