Matt:LabNotes/2015-4-15: Difference between revisions

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(Created page with "==Rank Correlation Between DARTFISH and FISSEQ== *Repeat these linear regressions with rank correlation to see if it c...")
 
>Mzcai
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   V4V7_GeneCounts$RankFISSEQv2 <- rank(V4V7_GeneCounts$FISSEQv2, 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")
   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")
  > cor.test(V4V7_GeneCounts$RankFISSEQv1, V4V7_GeneCounts$RankFISSEQv2, method="spearman")
 
Spearman's rank correlation rho
Spearman's rank correlation rho
 
  data:  V4V7_GeneCounts$RankFISSEQv1 and V4V7_GeneCounts$RankFISSEQv2
data:  V4V7_GeneCounts$RankFISSEQv1 and V4V7_GeneCounts$RankFISSEQv2
  S = 2198.517, p-value = 3.244e-08
S = 2198.517, p-value = 3.244e-08
  alternative hypothesis: true rho is not equal to 0
alternative hypothesis: true rho is not equal to 0
  sample estimates:
sample estimates:
       rho  
       rho  
0.7594357  
  0.7594357  
 
> cor.test(V4V7_GeneCounts$RankFISSEQv1, V4V7_GeneCounts$RankFibV4_Norm, method="spearman")


  > cor.test(V4V7_GeneCounts$RankFISSEQv1, V4V7_GeneCounts$RankFibV4_Norm, method="spearman")
Spearman's rank correlation rho
Spearman's rank correlation rho
 
  data:  V4V7_GeneCounts$RankFISSEQv1 and V4V7_GeneCounts$RankFibV4_Norm
data:  V4V7_GeneCounts$RankFISSEQv1 and V4V7_GeneCounts$RankFibV4_Norm
  S = 867037.8, p-value = 0.216
S = 867037.8, p-value = 0.216
  alternative hypothesis: true rho is not equal to 0
alternative hypothesis: true rho is not equal to 0
  sample estimates:
sample estimates:
       rho  
       rho  
0.09292391  
  0.09292391  
 
> cor.test(V4V7_GeneCounts$RankFibV4_Norm, V4V7_GeneCounts$RankFISSEQv2, method="spearman")


  > cor.test(V4V7_GeneCounts$RankFibV4_Norm, V4V7_GeneCounts$RankFISSEQv2, method="spearman")
Spearman's rank correlation rho
Spearman's rank correlation rho
 
  data:  V4V7_GeneCounts$RankFibV4_Norm and V4V7_GeneCounts$RankFISSEQv2
data:  V4V7_GeneCounts$RankFibV4_Norm and V4V7_GeneCounts$RankFISSEQv2
  S = 5811.43, p-value = 0.02462
S = 5811.43, p-value = 0.02462
  alternative hypothesis: true rho is not equal to 0
alternative hypothesis: true rho is not equal to 0
  sample estimates:
sample estimates:
       rho  
       rho  
0.3641066
  0.3641066

Revision as of 01:03, 16 April 2015

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