Functional Analysis ERROR and Target Prediction empty

[flyman0302]

I have get the following result. And I check the miRNAs targets that is empty. Please tell me what shall I do? [Thu Dec 7 09:54:52 2017] Starting a differential expression analysis using EdgeR-Noiseq software(s) [Thu Dec 7 09:57:32 2017] Differential expression analysis finished. [Thu Dec 7 09:57:32 2017] Starting a Functional Analysis. [Thu Dec 7 09:58:47 2017] ERROR :: Nothing significative was found using edgeR data. No Functional analisis result files were generated

[Thu Dec 7 09:59:56 2017] WARN :: The number of differentially expressed genes is too small (<50). Some errors could appear. Try to use a less restringet cut_off for noiseq(>0.7) [Thu Dec 7 09:59:56 2017] ERROR :: Nothing significative was found using noiseq data. No Functional analisis result files were generated

[Thu Dec 7 09:59:56 2017] Functional Analysis finished. [Thu Dec 7 09:59:56 2017] Starting a target Prediction Analysis using miRGate [Thu Dec 7 10:04:59 2017] Target Prediction Analysis finished. [Thu Dec 7 10:04:59 2017] miARma finished. Job took 10 minutes

[Eduardo Andres Leon]

Hi, Could you send me your ini, log files (both, stat.log and log) and the summary_XXX.xls ?

Kind regards

[flyman0302]

please check the attachments

[Eduardo Andres Leon]

Hi, I'm checking the module in charge of the "Target Prediction" section.

But I also suggest you to take a look to the parameters used in the Readcount part, your best % is nearly 15%. You can enter in the xxx_readcount_results (low case) folder. There you will find some xxx.tab.summary files with the number of assigned reads in different elements. Maybe you have to use parameters=-M -O in the ReadCount section

[Eduardo Andres Leon]

As fas as I know it seems a bioMaRt error:

> data_maRT<-as.data.frame(listDatasets(useMart("ENSEMBL_MART_ENSEMBL", host = "www.ensembl.org")))
> data_maRT[data_maRT$dataset=="hsapiens_gene_ensembl",]
             dataset              description    version
27 hsapiens_gene_ensembl Human genes (GRCh38.p10) GRCh38.p10
> ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="www.ensembl.org")
Error in checkDataset(dataset = dataset, mart = mart) : 
The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.
> data_maRT[data_maRT$dataset=="mmusculus_gene_ensembl",]
[1] dataset     description version    
<0 rows> (or 0-length row.names)
> ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="mmusculus_gene_ensembl", host="www.ensembl.org")
> ensembl
Object of class 'Mart':
  Using the ENSEMBL_MART_ENSEMBL BioMart database
  Using the mmusculus_gene_ensembl dataset

[Eduardo Andres Leon]

Hi again, Could you confirm that everything is working properly ? (BioMaRt is up and running at the moment)

[Eduardo Andres Leon]

No answer