Problem in preparing analysis

Enhanced tool for detecting CNVs from whole-exome sequencing data

Status: Beta

Brought to you by: albertomagi

#5 Problem in preparing analysis

Milestone: 1.0

Status: open

Owner: nobody

Labels: Excavator2 error (1) missing values and NaN's not allowed if 'na.rm' is FALSE (1) Calls: QuantileLength -> rbind -> quantile -> quantile.default (1)

Updated: 2017-09-25

Created: 2017-09-16

Creator: pradyumna J

Private: No

Hi,
I have this error message when I ran the following command to prepare the excavator files with my data
perl EXCAVATORDataPrepare.pl melas_prepare.txt --processors 6 --target melas20k --assembly hg19

Error Message:

Working on sample M1.
Creating Read Count Data...

Removing temporary files...
Read Count done!
Normalizing Read Count Data...
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: ‘Hmisc’

The following objects are masked from ‘package:base’:
format.pval, round.POSIXt, trunc.POSIXt, units
Error in quantile.default(RCTL[ind], c(0.1, 0.9)) :
missing values and NaN's not allowed if 'na.rm' is FALSE
Calls: QuantileLength -> rbind -> quantile -> quantile.default
Execution halted

Discussion

pradyumna J - 2017-09-25

This problem was solved by changing na.rm value from na.rm=T to na.rm=TRUE in the R scripts.

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Problem in preparing analysis

Enhanced tool for detecting CNVs from whole-exome sequencing data

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#5 Problem in preparing analysis

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