1) RSEM input
Having counts of RSEM for several samples, we compiled a table like described in e.g. the Trinity description into one table for all samples. Striuggeling now in DeSeq2 with the function "deseqtable <- DESeqDataSetFromMatrix" we tried now the tximport package reading the manual but again struggeling how to adjust the example "files <- file.path(dir, "rsem", samples$run, paste0(samples$run, ".genes.results"))"... which takes the counts from the RSEM output tables directly and somehow accounts for non-integers.
Isn't there an alternative way to e.g. import a table from all samples directly (RSEM_trans_iso_counts.counts.matrix)
in the following format
S1 S2 S3 S4
TRINITY_DN38912_c0_g1_i1 0.00 0.00 1.00 2.00
TRINITY_DN24712_c0_g1_i7 54.45 0.00 17.39 0.00
without rounding it first ?
Would be helpful if anyone can post some helpful command lines :)
2) is DeSeq2 by default excluding results with low counts (see 1.5.3) - how can I set different treshholds or turn off this filtering, by setting p-values set to NA ? (I got that a more strict filtering is
automatically applied via independent filtering on the mean of normalized counts
within the results function (section 3.8) how to change this?
thanks for help