I'm using tuxedo work flow to find DGE (ballgown) of RNAseq data control vs treated each with biological replicates. which one of the below matrix and stattest should be applied and why?
https://github.com/skptic/tuxedo-nf
any help would be appreciated, Thanks.
1.
sample condition Bioreplicate
sampleA Ctr rep1
sampleA Ctr rep2
sampleA Ctr rep3
sampleA Tre rep1
sampleA Tre rep2
sampleA Cre rep3
stat_results = stattest(bg, feature='transcript', meas='FPKM', covariate='condition', adjustvars=c('Bioreplicate'), getFC=TRUE)
2.
sample condition
sampleA Ctr
sampleA Ctr
sampleA Ctr
sampleA Tre
sampleA Tre
sampleA Tre
stat_results = stattest(bg, feature='transcript', meas='FPKM', covariate='condition', getFC=TRUE)
Another category two condition (control vs treated) from two different cell lines (a,b) with replicate (3).
Other than one of the above matrix to call control vs treated for each lines separately, I wanted to know genes which are diff.exp btn control vs treated in both cell lines. Could I use the below matrix?
1.
sample condition cell
sampleA Ctr cellA
sampleB Ctr cellA
sampleC Ctr cellA
sampleD Tre cellA
sampleE Tre cellA
sampleF Tre cellA
sampleG Ctr cellB
sampleH Ctr cellB
sampleI Ctr cellB
sampleJ Tre cellB
sampleK Tre cellB
sampleL Cre cellB
stat_results = stattest(bg, feature='transcript', meas='FPKM', covariate='condition', adjustvars=c('cell'), getFC=TRUE)
OR
stat_results = stattest(bg, feature='transcript', meas='FPKM', covariate='cell', adjustvars=c('condition), timecourse=TRUE, getFC=TRUE)