Matt:LabNotes/2015-4-15

From ZhangLabWiki
Revision as of 01:02, 16 April 2015 by >Mzcai (Created page with "==Rank Correlation Between DARTFISH and FISSEQ== *Repeat these linear regressions with rank correlation to see if it c...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

Rank Correlation Between DARTFISH and FISSEQ

  • Repeat these linear regressions with rank correlation to see if it can improve p-value
    • Since relationship between DARTFISH and FISSEQ is not expected to be linear, rank correlation may be more appropriate
  • Workspace: "C:\Users\Matt\Dropbox\GradZhangLab\DecodeData\ReferenceData\.RData"

Spearman's Correlation

 V4V7_GeneCounts$RankFISSEQv1 <- rank(V4V7_GeneCounts$FISSEQv1, na.last="keep",ties.method="average")
 V4V7_GeneCounts$RankFISSEQv2 <- rank(V4V7_GeneCounts$FISSEQv2, na.last="keep",ties.method="average")
 V4V7_GeneCounts$RankFibV4_Norm <- rank(V4V7_GeneCounts$FibV4_Norm, na.last="keep",ties.method="average")

> cor.test(V4V7_GeneCounts$RankFISSEQv1, V4V7_GeneCounts$RankFISSEQv2, method="spearman")

Spearman's rank correlation rho

data: V4V7_GeneCounts$RankFISSEQv1 and V4V7_GeneCounts$RankFISSEQv2 S = 2198.517, p-value = 3.244e-08 alternative hypothesis: true rho is not equal to 0 sample estimates:

     rho 

0.7594357

> cor.test(V4V7_GeneCounts$RankFISSEQv1, V4V7_GeneCounts$RankFibV4_Norm, method="spearman")

Spearman's rank correlation rho

data: V4V7_GeneCounts$RankFISSEQv1 and V4V7_GeneCounts$RankFibV4_Norm S = 867037.8, p-value = 0.216 alternative hypothesis: true rho is not equal to 0 sample estimates:

      rho 

0.09292391

> cor.test(V4V7_GeneCounts$RankFibV4_Norm, V4V7_GeneCounts$RankFISSEQv2, method="spearman")

Spearman's rank correlation rho

data: V4V7_GeneCounts$RankFibV4_Norm and V4V7_GeneCounts$RankFISSEQv2 S = 5811.43, p-value = 0.02462 alternative hypothesis: true rho is not equal to 0 sample estimates:

     rho 

0.3641066