Matt:LabNotes/2015-4-15: Difference between revisions
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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") | ||
*FISSEQv1 vs FISSEQv2 | |||
> 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 | |||
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 | ||
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rho | rho | ||
0.7594357 | 0.7594357 | ||
*FISSEQv1 vs DARTFISH | |||
> 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 | |||
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 | ||
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rho | rho | ||
0.09292391 | 0.09292391 | ||
*FISSEQv2 vs DARTFISH | |||
> 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 | |||
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 | ||
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rho | rho | ||
0.3641066 | 0.3641066 | ||
*Could potentially improve correlation by not ranking genes in DARTFISH that are not present in FISSEQ... |
Latest revision as of 01:05, 16 April 2015
Rank Correlation Between DARTFISH and FISSEQ[edit]
- 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[edit]
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")
- FISSEQv1 vs FISSEQv2
> 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
- FISSEQv1 vs DARTFISH
> 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
- FISSEQv2 vs DARTFISH
> 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
- Could potentially improve correlation by not ranking genes in DARTFISH that are not present in FISSEQ...