search

kundajelab / DMSO

5 stars 3 forks source link

Surrogate variable analysis for top 2 candidate models #4

Open annashcherbina opened 7 years ago

annashcherbina commented 7 years ago

Heatmaps for 75 cell cycle genes before and after removal of surrogate variables:

Using rlog(counts):

Using asinh(tpm)

Cumulative distribution of expression values pre- and post- sva removal:

cdf_distributions

The rlog-transformed data has a tighter overlap among the samples.

annashcherbina commented 7 years ago

-10log10(FDR) vs logFC

pval_and_log earlyg1 pval_and_log earlyg1_vs_gs2m_c pval_and_log earlyg1_vs_sg2m_t pval_and_log lateg1 pval_and_log lateg1_vs_earlyg1_c pval_and_log lateg1_vs_earlyg1_t pval_and_log sg2m pval_and_log sg2m_vs_lateg1_c pval_and_log sg2m_vs_lateg1_t

annashcherbina commented 7 years ago

RANKS

ranks earlyg1 ranks earlyg1_vs_gs2m_c ranks earlyg1_vs_sg2m_t ranks lateg1 ranks lateg1_vs_earlyg1_c ranks lateg1_vs_earlyg1_t ranks sg2m ranks sg2m_vs_lateg1_c ranks sg2m_vs_lateg1_t

annashcherbina commented 7 years ago

Volcano plots

volcano earlyg1 volcano earlyg1_vs_gs2m_c volcano earlyg1_vs_sg2m_t volcano lateg1 volcano lateg1_vs_earlyg1_c volcano lateg1_vs_earlyg1_t volcano sg2m volcano sg2m_vs_lateg1_c volcano sg2m_vs_lateg1_t

annashcherbina commented 7 years ago

Venn

venn earlyg1 venn earlyg1_vs_gs2m_c venn earlyg1_vs_sg2m_t venn lateg1 venn lateg1_vs_earlyg1_c venn lateg1_vs_earlyg1_t venn sg2m venn sg2m_vs_lateg1_c venn sg2m_vs_lateg1_t