ZW-xjtlu
commented
2 years ago exomePeak2的使用者您好，这个BUG是源于保存BED文件时出现了值为NA的-log10 values，以至于后续步骤无法运行, 我将于今天之内修复这个问题并通知您。
On May 15, 2022, at 1:49 AM, ZehongW @.**@.>> wrote:
作者您好，我最近用新版exomePeak2的时候报了这样的错： Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Extract bin features ... OK Count reads on bin features ... OK Identify background features ... OK Estimate sample sepecific size factors from the background ... OK Detect peaks with GLM ... OK Count reads on peaks ... OK Calculate offset matrix for peaks ... OK Detect differentially modified peaks with interactive GLM ... OK Error in .local(object, con, format, ...) : Scores must be non-NA numeric values Calls: exomePeak2 ... callGeneric -> eval -> eval -> export -> export -> .local
以下是我的代码（3个重复）： library(exomePeak2)
setwd("/home/wuzh/shMETTL14") GENE_ANNO_GTF = '/home/wuzh/hisat2_index/hg19/hg19.gtf'
control_Input = c('siControl_1_input.bam','siControl_2_input.bam','siControl_3_input.bam') control_IP = c('siControl_1_IP.bam','siControl_2_IP.bam','siControl_3_IP.bam')
shmettl14_Input = c('siMETTL14_1_input.bam','siMETTL14_2_input.bam','siMETTL14_3_input.bam') shmettl14_IP = c('siMETTL14_1_IP.bam','siMETTL14_2_IP.bam','siMETTL14_3_IP.bam')
sep1 <- exomePeak2( bam_ip = control_IP, bam_input = control_Input, bam_ip_treated = shmettl14_IP, bam_input_treated = shmettl14_Input, gff = GENE_ANNO_GTF,
genome = "hg19",
strandness = "1st_strand", parallel = 12, save_output = TRUE, save_dir = getwd(), experiment_name = "exomePeak2_updated_output_shmettl14") 之前用两个重复的时候好像可以跑通，挺疑惑的。希望您能帮我看一下，十分感激！
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ZehongW
hlldhy
作者您好，我最近用新版exomePeak2的时候报了这样的错： Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Extract bin features ... OK Count reads on bin features ... OK Identify background features ... OK Estimate sample sepecific size factors from the background ... OK Detect peaks with GLM ... OK Count reads on peaks ... OK Calculate offset matrix for peaks ... OK Detect differentially modified peaks with interactive GLM ... OK Error in .local(object, con, format, ...) : Scores must be non-NA numeric values Calls: exomePeak2 ... callGeneric -> eval -> eval -> export -> export -> .local
以下是我的代码（3个重复）： library(exomePeak2)
setwd("/home/wuzh/shMETTL14") GENE_ANNO_GTF = '/home/wuzh/hisat2_index/hg19/hg19.gtf'
control_Input = c('siControl_1_input.bam','siControl_2_input.bam','siControl_3_input.bam') control_IP = c('siControl_1_IP.bam','siControl_2_IP.bam','siControl_3_IP.bam')
shmettl14_Input = c('siMETTL14_1_input.bam','siMETTL14_2_input.bam','siMETTL14_3_input.bam') shmettl14_IP = c('siMETTL14_1_IP.bam','siMETTL14_2_IP.bam','siMETTL14_3_IP.bam')
sep1 <- exomePeak2( bam_ip = control_IP, bam_input = control_Input, bam_ip_treated = shmettl14_IP, bam_input_treated = shmettl14_Input, gff = GENE_ANNO_GTF,
genome = "hg19",
之前用两个重复的时候好像可以跑通，挺疑惑的。希望您能帮我看一下，十分感激！