mRNA EDA: PCA and correlation plots of postnormalized expression data, RemapYear1
This document has last been compiled on 2021-12-14 21:23:58.
## Reading in metadata from file: results/RemapYear1/data/root_meta.txt
## Reading in data from file: results/RemapYear1/data/root_normCounts.txt## Total number of root samples: 194
## Total number of genes in root samples: 22177
## No additional bad samples to remove (probably removed during normalization)
## There are no samples to remove beyond those used in the main experiment
## Variance filter for root samples: Remove genes in the bottom 0.25 quantile of variability
## Total number of genes after limiting to high variable genes : 16632
## After filtering root samples: 194 samples, 16632 genes## Reading in metadata from file: results/RemapYear1/data/leaf_meta.txt
## Reading in data from file: results/RemapYear1/data/leaf_normCounts.txt## Total number of leaf samples: 197
## Total number of genes in leaf samples: 20198
## No additional bad samples to remove (probably removed during normalization)
## There are no samples to remove beyond those used in the main experiment
## Variance filter for leaf samples: Remove genes in the bottom 0.25 quantile of variability
## Total number of genes after limiting to high variable genes : 15148
## After filtering leaf samples: 197 samples, 15148 genesNote that when we are using NORMALIZED data (leaf and root separately), we are using the leaf (root) data file that is the default of bringInDataFunction, the NORMALIZED fpkm values; for this data (leaf and root separately) we are filtering by expression and also on variance within those subsets of samples.
Note that the comments for Year1 that follow are based on the original identification of mislabeled samples; some of these (with swapped labels) have been rerun on on the correct genotype and no longer show up as mislabeled, so this file is out of date in that respect.
RLE plots
## Day007 Day014 Day021 Day028 Day035 Day042 Day049 Day056
## "#00FF00" "#0BD55F" "#16ABBF" "#2F8EFF" "#6489FF" "#9983FF" "#A66DF2" "#A050DF"
## Day057 Day058 Day059 Day061 Day063 Day064 Day065 Day066
## "black" "black" "black" "black" "black" "black" "black" "black"
## Day068 Day070 Day077 Day084 Day091 Day098 Day105 Day112
## "black" "#D30000" "#A70000" "#991804" "#C46012" "#F0A820" "#FFD01B" "#FFE70D"
## Day119
## "#FFFF00"## Root:##
## Control Postflowering Preflowering
## Day014 6 0 0
## Day021 6 0 6
## Day028 6 0 6
## Day035 6 0 6
## Day042 6 0 6
## Day049 2 0 2
## Day056 6 0 3
## Day063 6 6 6
## Day070 6 6 6
## Day077 6 6 6
## Day084 5 2 6
## Day091 4 6 6
## Day098 2 2 2
## Day105 5 6 4
## Day112 1 2 2
## Day119 6 6 6## Leaf:##
## Control Postflowering Preflowering
## Day014 6 0 0
## Day021 6 0 6
## Day028 5 0 6
## Day035 6 0 5
## Day042 6 0 6
## Day049 2 0 2
## Day056 6 0 6
## Day063 6 6 6
## Day070 6 6 6
## Day077 6 6 6
## Day084 6 2 6
## Day091 6 6 6
## Day098 2 2 2
## Day105 5 6 4
## Day112 1 1 2
## Day119 6 6 6
PCA of Expression Values
PCA on Leaves
PCA on Roots
Correlation Matrices of mRNA data
Correlation of all samples, Leaf
## Barcode libraryName Block Week Replicate Genotype Condition
## 0914167L02 0914167L02 BOCUN Block 02 Week15 1 BT642 Control
## Sample.type Day Genotype.Sample.type CompleteTreatment
## 0914167L02 Leaves Day105 BT642:Leaves BT642:Day105:Control:Leaves
## Row isFloweringWeek Year Time.Point Date.Harvested
## 0914167L02 Row7 NA Year1 105 9/14/16
## Collected.By Collection.Time No.plants.pooled Notes
## 0914167L02 Israeal/Raoul/Julie 10:34 AM 10
## Time.Factor mainExperiment FloweringJulianDate FloweringDate
## 0914167L02 Day105 TRUE NA <NA>
## FloweringWeek FloweringDay FloweringJulianDate.1
## 0914167L02 NA NA NA
## LbsGrainHarvestPerPlot TonsOfGrain.ac PctGrainMoisture
## 0914167L02 NA NA NA
## TonsOfGrain.acAt13PctMoisture X1000SeedWt_g
## 0914167L02 NA NA
## ApproximateEndOfSeasonStandCount_aveOfGrainRows
## 0914167L02 NA
## TotalFreshForageWtPerPlot_kg TotalFreshForageWtPerPlot_lbs
## 0914167L02 NA NA
## TonsOfForage.ac PctMoistureForage TonsOfForage.acAt65PctMoisture
## 0914167L02 NA NA NA
## ApproximateEndOfSeasonStandCount_aveOfForageRows DryBiomass
## 0914167L02 NA NA
## FreshBiomass AveHeight Station Precip Air.max Air.min Air.avg
## 0914167L02 NA NA PARLIER.A 0 82 49 65.5
## Soil.max Soil.min Soil.avg Solar ETo RH.max RH.min BarcodeJGI
## 0914167L02 75 69 72 525 0.17 84 26 0914167L02
## isCorrectedBarcode SampleId rawReads filteredReads sampleName
## 0914167L02 FALSE 131927 11838602 11812642 0914167L02
## conditionNumber sequencerType runType
## 0914167L02 7 HiSeq-2500 1TB 1x101
## fileUsed processed_as
## 0914167L02 11198.7.195894.CACGTTG-ACAACGT.filter-RNA.fastq.gz BT642
## totalFragments mappedFragments assignedFragments unassignedAmbiguous
## 0914167L02 27647085 2080902 1907960 14548
## unassignedNoFeatures unassignedSecondaryHits ratioStrandedness
## 0914167L02 158394 0 0.9761
## MappedRatio AssignedRatio Plate1 Plate.Location Plate
## 0914167L02 0.0752666 0.06901125 16-Dec-13_RA_1 G6 G
## Genotype.Original Mislabeled Unreplicated badSamples
## 0914167L02 BT642 FALSE FALSE FALSE
## questionableSamples CompleteSampleTreatment Genotype.Corrected
## 0914167L02 FALSE BT642:Day105:Control BT642
Correlation of all samples, Root
## [1] Barcode
## [2] libraryName
## [3] Block
## [4] Week
## [5] Replicate
## [6] Genotype
## [7] Condition
## [8] Sample.type
## [9] Day
## [10] Genotype.Sample.type
## [11] CompleteTreatment
## [12] Row
## [13] isFloweringWeek
## [14] Year
## [15] Time.Point
## [16] Date.Harvested
## [17] Collected.By
## [18] Collection.Time
## [19] No.plants.pooled
## [20] Notes
## [21] Time.Factor
## [22] mainExperiment
## [23] FloweringJulianDate
## [24] FloweringDate
## [25] FloweringWeek
## [26] FloweringDay
## [27] FloweringJulianDate.1
## [28] LbsGrainHarvestPerPlot
## [29] TonsOfGrain.ac
## [30] PctGrainMoisture
## [31] TonsOfGrain.acAt13PctMoisture
## [32] X1000SeedWt_g
## [33] ApproximateEndOfSeasonStandCount_aveOfGrainRows
## [34] TotalFreshForageWtPerPlot_kg
## [35] TotalFreshForageWtPerPlot_lbs
## [36] TonsOfForage.ac
## [37] PctMoistureForage
## [38] TonsOfForage.acAt65PctMoisture
## [39] ApproximateEndOfSeasonStandCount_aveOfForageRows
## [40] DryBiomass
## [41] FreshBiomass
## [42] AveHeight
## [43] Station
## [44] Precip
## [45] Air.max
## [46] Air.min
## [47] Air.avg
## [48] Soil.max
## [49] Soil.min
## [50] Soil.avg
## [51] Solar
## [52] ETo
## [53] RH.max
## [54] RH.min
## [55] BarcodeJGI
## [56] isCorrectedBarcode
## [57] SampleId
## [58] rawReads
## [59] filteredReads
## [60] sampleName
## [61] conditionNumber
## [62] sequencerType
## [63] runType
## [64] fileUsed
## [65] processed_as
## [66] totalFragments
## [67] mappedFragments
## [68] assignedFragments
## [69] unassignedAmbiguous
## [70] unassignedNoFeatures
## [71] unassignedSecondaryHits
## [72] ratioStrandedness
## [73] MappedRatio
## [74] AssignedRatio
## [75] Plate1
## [76] Plate.Location
## [77] Plate
## [78] Genotype.Original
## [79] Mislabeled
## [80] Unreplicated
## [81] badSamples
## [82] questionableSamples
## [83] CompleteSampleTreatment
## [84] Genotype.Corrected
## <0 rows> (or 0-length row.names)