Matt:LabNotes/2015-4-15: Difference between revisions
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>Mzcai (Created page with "==Rank Correlation Between DARTFISH and FISSEQ== *Repeat these linear regressions with rank correlation to see if it c...") |
>Mzcai mNo edit summary |
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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") | |||
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") | |||
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