QSEA Error while loading the bam files
1
0
Entering edit mode
geekyvt • 0
@geekyvt-15045
Last seen 3.9 years ago

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, 

qsea • 729 views
ADD COMMENT
1
Entering edit mode
@matthias-lienhard-6292
Last seen 8 months ago
Max Planck Institute for molecular Gene…

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 COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 218 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6