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===Linear Regressions=== *Compare to regressions with gDNA in vitro normalized DARTFISH counts: [[Matt:LabNotes/2015-4-8]] ====Gene Counts: V4 vs V7 in vitro Capture==== *Previously (left/top fig.) very different gene count distributions between V4 and V7 caused the correlation between V4 and V7 DARTFISH gene counts in PGP1f to have no correlation *Now (right/bottom fig.) gene count between V4 and V7 in vitro capture is much better, but maybe only because both were divided by same FPKM values lm(loginvitro_cV7_Norm~loginvitro_cV4_Norm, data = V4V7_GeneCounts, na.action=na.omit) [[File:Regression_invitrocounts_V4_vs_V7.jpeg]] [[File:Regression_NormalizedcDNA_invitrocounts_V4_vs_V7.png |550px]] ====PGP1f: V4 vs V7 (cDNA invitro normalized)==== [[File:PGP1f_log_cDNAnorm_V4_vs_V7.png |550px]] *Much better correlation than when DARTFISH counts normalized by gDNA in vitro counts [[File:PGP1f_log_norm_V4_vs_V7.jpeg |350px]] ====PGP1f vs BA8 (V4, cDNA invitro normalized)==== [[File:V4_log_cDNAnorm_PGP1f_vs_BA8.png |550px]] *Such high correlation between different samples is not a positive result... ====PGP1f: DARTFISH (V4, cDNA invitro normalized) vs RNA-Seq==== [[File:PGP1fV4_logDARTFISH_cDNAnorm_vs_logRNASeq_regression.png |550px]] ====PGP1f: DARTFISH (V7, cDNA invitro normalized) vs RNA-Seq==== [[File:PGP1fV7_logDARTFISH_cDNAnorm_vs_logRNASeq_regression.png |550px]] *V7 is improved over gDNA invitro normalization (used to be negatively correlated) but still worse than V4 ====PGP1f: DARTFISH (V4, cDNA invitro normalized) vs RNA-Seqv2==== [[File:PGP1fV4_logDARTFISH_cDNAnorm_vs_logRNASeqv2_regression.png |550px]] ====PGP1f: DARTFISH (V4, cDNA invitro normalized) vs BeadArray==== *Using: FPKM for gene = max FPKM of gene's isoforms [[File:PGP1fV4_logDARTFISH_cDNAnorm_vs_logBeadArrayMax_regression.png |550px]] ====PGP1f: DARTFISH (V4, cDNA invitro normalized) vs FISSEQ==== [[File:PGP1fV4_logDARTFISH_cDNAnorm_vs_logFISSEQv1_regression.png |550px]] ====PGP1f: DARTFISH (V4, cDNA invitro normalized) vs FISSEQv2==== [[File:PGP1fV4_logDARTFISH_cDNAnorm_vs_logFISSEQv2_regression.png |550px]] ====BA8: DARTFISH vs RNA-Seq==== [[File:BA8_logDARTFISH_cDNAnorm_vs_logRNASeqBulkT_regression.png |550px]] *Got worse from gDNA in vitro normalization: R^2 = 0.2
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