Question: error while running MAplot
0
gravatar for Kritika
3.4 years ago by
Kritika260
India
Kritika260 wrote:

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 ?

rna-seq cummerbund maplot • 769 views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Kritika260
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