Hi all,
First post here, so apologies if I haven't explained anything clearly/followed standard guidelines.
I'd like to create a summarized experiment object for downstream analysis of my count data from RNA seq analysis. The way I do this is something like this:
rna_raw_counts_no_tech_rep_ordered.se <- SummarizedExperiment(list(rna_raw_counts_no_tech_rep_ordered), rowRanges = exons.genes)Where rna_raw_counts_no_tech_rep_ordered is my table of raw counts across all samples. exons.genes is a GRanges list which looks like this (one example gene; this contains ranges for the whole genome of interest):
$00R_Pgap2
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
[1] chr7 [102235854, 102235872] +
[2] chr7 [102236094, 102236346] +
[3] chr7 [102236448, 102236542] +
[4] chr7 [102237122, 102237230] +
[5] chr7 [102237401, 102237530] +
However, I notice that when I add the rowRanges argument to the SummarizedExperiment function as shown above, my counts across all samples change! When it isn't included, the counts stay the same as what's in the raw count table. I can access the counts like this:
assaysrna_raw_counts_no_tech_rep_ordered.se)[[1]]["00R_Pgap2 ",]
Has anyone come across an error like this? Thanks very much for your help!
Can you provide a reproducible example? For instance, I hae
> library(SummarizedExperiment) > m <- matrix(1:4, 2, dimnames=list(letters[1:2], NULL)) > rowRanges <- GRanges("chr1", IRanges(1:2, 3, names=letters[1:2])) > assay(SummarizedExperiment(list(m), rowRanges=rowRanges)) [,1] [,2] a 1 3 b 2 4Also, it's important to make sure we're using current software, so I have