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Question: QSEA Error while loading the bam files
0
gravatar for geekyvt
9 months ago by
geekyvt0
geekyvt0 wrote:

Hi,

I am using QSEA and while loading bam files, I am getting error like this... What could be the possible error...??

Error in validObject(.Object) : 
 invalid class “PhredQuality” object: undefined class for slot "elementMetadata" ("DataTableORNULL")

 

 

My script goes lik below,

sample_name <- c("N", "T")
file_name <- c("N_Cleaned.bam", "T_Cleaned.bam")
group <- c("Normal", "Tumor")
sex <- c("female", "female")
samples_NSCLC <- data.frame(sample_name, file_name, group, sex)

Chromosomes = paste0("chr", 1:22)
Chromosomes <- c(Chromosomes, "chrM", "chrX", "chrY")

qseaSet=createQseaSet(sampleTable=samples_NSCLC, BSgenome="BSgenome.Hsapiens.UCSC.hg19", chr.select=Chromosomes, window_size=500)

and getting above mentioned error, 

ADD COMMENTlink modified 9 months ago by Matthias Lienhard140 • written 9 months ago by geekyvt0
1
gravatar for Matthias Lienhard
9 months ago by
Max Planck Institute for molecular Genetics, Berlin, Germany
Matthias Lienhard140 wrote:

Hi geekyvt,

I could not reproduce the error. As long as the two bam files are present, your script does not produce an error for me. Can you please confirm that you are using the latest version of bioconductor, along with the corresponding version of R? Also, in the ceateQseaSet step, only the presence of the bam files are checked, otherwise they are not touched here. The expected behavior would be:

> qseaSet=createQseaSet(sampleTable=samples_NSCLC, BSgenome="BSgenome.Hsapiens.UCSC.hg19", chr.select=Chromosomes, window_size=500)
==== Creating qsea set ====
restricting analysis on chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrM, chrX, chrY
Dividing selected chromosomes of BSgenome.Hsapiens.UCSC.hg19 in 500nt windows
>

or, if the files are not present in the working directory:

Error in checkSampleTab(sampleTable) : Input file check failed:
File not found: N_Cleaned.bam
File not found: T_Cleaned.bam

Best, Matthias

ADD COMMENTlink written 9 months ago by Matthias Lienhard140

Thank you so much, Matthias. It really helped me a lot. I have updated all modules and it started working like a charm.

thanks,

Vivek

ADD REPLYlink written 9 months ago by geekyvt0

Hi Vivek,

I am happy to hear that it works now. Can you please "accept" the answer if your issue is fully solved?

Best, Matthias

ADD REPLYlink written 9 months ago by Matthias Lienhard140
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