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, 

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