Hi,

I previously used EasyRNASeq 1.8 to get count matrices from BAM files with a simple write.table command. I am trying to move to v. 2.0.8 but I just can’t seem to be able to do the same with the SummerizedExperiment object created…  I know that I could create object sot feed directly to edgeR or deseq2 but we want to do our own analysis with various other techniques.

Probably a trivial thing but I am no R/Bioconductor wizard ;-)

Thanks in advance

Sylvain

Hi Andrzej,

It does not provide meaningful info:

> ?SummarizedExperiment

No documentation for ‘SummarizedExperiment’ in specified packages and libraries:

you could try ‘??SummarizedExperiment’

> ??SummarizedExperiment

Help files with alias or concept or title matching

‘SummarizedExperiment’ using fuzzy matching:

easyRNASeq::BamFileList

                        Count summarization and normalization pipeline

                        for Next Generation Sequencing data.

biovizBase::mold        mold data into data.frame

DESeq2::collapseReplicates

                        Collapse replicates in a SummarizedExperiment

                        or DESeqDataSet

GenomicRanges::SummarizedExperiment-class

                        SummarizedExperiment instances

Type '?PKG::FOO' to inspect entries 'PKG::FOO', or 'TYPE?PKG::FOO' for

entries like 'PKG::FOO-TYPE'.

What's next?

S

Hi Sylvain,

you can use the assays method to extract the count table from your SummerizedExperiment object, for details see ?SummarizedExperiment.

Best,

Andrzej