Functional Analysis ERROR and Target Prediction empty
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
Comments (8)
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reporter - attached miARma_logfile.36955.log
- attached miARma_stat.36955.log
- attached miARma_mRNAs_test_Hisat2.ini
- attached summary_results_zhouyibo_lncRNA_miARma.xls
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reporter please check the attachments
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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
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assigned issue to
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assigned issue to
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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
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Hi again, Could you confirm that everything is working properly ? (BioMaRt is up and running at the moment)
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Hi, Could you send me your ini, log files (both, stat.log and log) and the summary_XXX.xls ?
Kind regards