error while running MAplot
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@kritikamish99-9648
Last seen 3.2 years ago
India

Hello all

i am running cummeRbund and i got error saying

Error in dat$x + pseudocount : non-numeric argument to binary operator

this is my command:-

cuff_1with2_for_cummeRbund <- readCufflinks(dir="/home/work/cuffdiff_out/cuffdiff_1with2_out/cuffdiff_result/",bdFile="cuffData.db",gtfFile = NULL,runInfoFile = "run.info", repTableFile = "read_groups.info",geneFPKM = "genes.fpkm_tracking", geneDiff = "gene_exp.diff", geneCount="genes.count_tracking", geneRep="genes.read_group_tracking",isoformFPKM = "isoforms.fpkm_tracking", isoformDiff = "isoform_exp.diff", isoformCount="isoforms.count_tracking", isoformRep="isoforms.read_group_tracking",TSSFPKM = "tss_groups.fpkm_tracking", TSSDiff = "tss_group_exp.diff", TSSCount="tss_groups.count_tracking", TSSRep="tss_groups.read_group_tracking",CDSFPKM = "cds.fpkm_tracking", CDSExpDiff = "cds_exp.diff", CDSCount="cds.count_tracking", CDSRep="cds.read_group_tracking",CDSDiff = "cds.diff",promoterFile = "promoters.diff", splicingFile = "splicing.diff",varModelFile = "var_model.info",driver = "SQLite", genome = NULL, rebuild = FALSE)

>cuff_1with2_for_cummeRbund

output :-

CuffSet instance with:
     2 samples
     4109 genes
     4109 isoforms
     0 TSS
     0 CDS
     0 promoters
     0 splicing
     0 relCDS

>ma_plot_1with2 <- MAplot(genes(cuff_1with2_for_cummeRbund),"sample_1","sample_2",pseudocount = 1,smooth=FALSE)

output:-

Error in dat$x + pseudocount : non-numeric argument to binary operator

 

any help ?

MAplot rnaseq cummerbund • 681 views
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