inst/RTqPCR.gui/result_report.md

In NPhogat/RTqPCR: A work flow for analysis and normalization of pre-processing RT-qPCR data

RT-qPCR (Real-Time Quantitative Polymerase Chain Reaction) Analysis Report

Date: 2017-05-15 23:22:50

Cq values and amplification efficiencies:

| | Cq| Efficiency| |:------|-----:|----------:| |1 | 45.00| 1.0024| |2 | NA| NA| |3 | 24.87| 0.6576| |4 | 29.37| 1.0004| |5 | NA| NA| |6 | 12.36| 0.5978| |7 | 2.49| 1.0001| |8 | NA| NA| |9 | 20.69| 0.5883| |10 | NA| NA| |11 | NA| NA| |12 | 21.16| 0.6202| |13 | NA| NA| |14 | NA| NA| |15 | 18.20| 0.5485| |16 | NA| NA| |17 | NA| NA| |18 | 18.69| 0.6362| |19 | NA| NA| |20 | NA| NA| |21 | 18.50| 1.1000| |22 | 1.00| 1.0000| |23 | 25.70| 2209.6000| |24 | NA| NA| |25 | NA| NA| |26 | NA| NA| |27 | 24.20| 0.6319| |28 | NA| NA| |29 | NA| NA| |30 | 1.00| 0.0905| |31 | NA| NA| |32 | 7.94| 0.2811| |33 | NA| NA| |34 | 1.87| 0.8794| |35 | NA| NA| |36 | 13.43| 0.6632| |37 | 11.00| 0.3586| |38 | NA| NA| |39 | 18.43| 1.0945| |40 | NA| NA| |41 | NA| NA| |42 | 20.09| 1.0956| |43 | 28.92| 1.0477| |44 | NA| NA| |45 | 12.61| 0.5111| |46 | NA| NA| |47 | NA| NA| |48 | NA| NA| |49 | NA| NA| |50 | NA| NA| |51 | 23.78| 0.6555| |52 | NA| NA| |53 | NA| NA| |54 | 15.95| 0.5482| |55 | NA| NA| |56 | NA| NA| |57 | NA| NA| |58 | 17.25| 0.5517| |59 | NA| NA| |60 | 21.98| 0.7010| |61 | NA| NA| |62 | NA| NA| |63 | 19.30| 1.0970| |64 | 17.12| 1.0912| |65 | NA| NA| |66 | 21.54| 0.6473| |67 | 14.67| 0.6436| |68 | NA| NA| |69 | 14.59| 0.7494| |70 | NA| NA| |71 | NA| NA| |72 | 15.30| 0.6284| |73 | NA| NA| |74 | 29.30| 0.9781| |75 | 12.15| 1.1753| |76 | NA| NA| |77 | NA| NA| |78 | 6.72| 0.9844| |79 | 5.85| 0.7985| |80 | 10.20| 0.9877| |81 | 10.76| 0.9879| |82 | 18.09| 1.0917| |83 | NA| NA| |84 | 26.82| 0.9920| |85 | NA| NA| |86 | 31.07| 1.2339| |87 | 29.58| 0.8596| |88 | 13.58| 1.1321| |89 | NA| NA| |90 | NA| NA| |91 | 11.15| 1.1839| |92 | 16.46| 0.9772| |93 | 9.23| 0.9801| |94 | 6.91| 0.9790| |95 | 8.05| 0.8942| |96 | NA| NA|

Cq values and amplification efficiencies after replacing above cut offs by nondetects (NA):

[1] "Select option other than 'None' and fill up necessary boxes to implement the method!"

Cq values and amplification values after replacing nondetects by user defined value:

[1] "Select option other than 'None' and fill up necessary boxes to implement the method!"

Cq values and amplification efficiencies after replacing specific values:

[1] "Select option other than 'None' and fill up necessary boxes to implement the method!"

Cq values and amplification efficiencies after removing the nondetects within replicates (method- mean or median):

[1] "Select option other than 'None' to implement the method!"

Combining technical replicates based on Cq values and S.D. of Cq values within replicates:

|ID |Cq |sd.Cq | |:------|:-----|:------| |1 |37.19 |11.052 | |3 |18.62 |8.846 | |7 |2.49 |NA | |9 |20.93 |0.332 | |15 |18.44 |0.245 | |21 |18.50 |NA | |22 |14.96 |19.742 | |23 |25.70 |NA | |27 |12.60 |16.405 | |32 |7.94 |NA | |34 |1.87 |NA | |36 |13.43 |NA | |37 |11.00 |NA | |42 |20.09 |NA | |45 |12.61 |NA | |51 |17.96 |8.224 | |54 |11.33 |6.527 | |58 |17.67 |0.594 | |60 |19.55 |3.437 | |63 |19.30 |NA | |66 |17.14 |3.824 | |67 |10.26 |6.237 | |74 |29.30 |NA | |80 |10.48 |0.396 | |84 |26.82 |NA | |86 |30.32 |1.054 | |88 |13.58 |NA | |91 |12.28 |3.745 | |94 |6.91 |NA | |95 |8.05 |NA |

Combining technical replicates based on efficiencies and S.D. of Cq and efficiencies within replicates:

|ID |Cq |sd.Cq |effs |sd.effs | |:------|:-----|:------|:--------|:--------| |1 |37.19 |11.052 |1.001 |0.001466 | |3 |18.62 |8.846 |0.628 |0.042348 | |7 |2.49 |NA |1.000 |NA | |9 |20.93 |0.332 |0.604 |0.022614 | |15 |18.44 |0.245 |0.760 |0.293195 | |21 |18.50 |NA |1.100 |NA | |22 |14.96 |19.742 |1.024 |0.033736 | |23 |25.70 |NA |2209.600 |NA | |27 |12.60 |16.405 |0.361 |0.382880 | |32 |7.94 |NA |0.281 |NA | |34 |1.87 |NA |0.879 |NA | |36 |13.43 |NA |0.663 |NA | |37 |11.00 |NA |0.359 |NA | |42 |20.09 |NA |1.096 |NA | |45 |12.61 |NA |0.511 |NA | |51 |17.96 |8.224 |0.915 |0.367514 | |54 |11.33 |6.527 |0.766 |0.308475 | |58 |17.67 |0.594 |0.822 |0.381787 | |60 |19.55 |3.437 |0.896 |0.275894 | |63 |19.30 |NA |1.097 |NA | |66 |17.14 |3.824 |0.675 |0.065095 | |67 |10.26 |6.237 |0.721 |0.109550 | |74 |29.30 |NA |0.978 |NA | |80 |10.48 |0.396 |0.988 |0.000168 | |84 |26.82 |NA |0.992 |NA | |86 |30.32 |1.054 |1.047 |0.264689 | |88 |13.58 |NA |1.132 |NA | |91 |12.28 |3.745 |1.047 |0.118480 | |94 |6.91 |NA |0.979 |NA | |95 |8.05 |NA |0.894 |NA |

Delta Cq values:

| |ID |deltaCq |sd.deltaCq | |:--|:------|:---------|:----------| |8 |23 |8.03429 |NA | |10 |32 |-9.72571 |NA | |23 |74 |11.63429 |NA | |26 |86 |12.65429 |6.07 | |28 |91 |-5.38571 |7.06 | |29 |94 |-10.75571 |NA | |30 |95 |-9.61571 |NA | |7 |22 |-2.70571 |20.63 | |11 |34 |-15.79571 |NA | |13 |37 |-6.66571 |NA | |27 |88 |-4.08571 |NA |

Delta Delta Cq values and fold concentrations of target samples:

|ID |deltadeltaCq |Fold Conc.[log] |sd.deltadeltaCq | |:------|:------------|:---------------|:---------------| |23 |15.35 |-10.64 |NA | |32 |-2.41 |1.67 |NA | |74 |18.95 |-13.14 |NA | |86 |19.97 |-13.84 |21.5 | |91 |1.93 |-1.34 |21.8 | |94 |-3.44 |2.38 |NA | |95 |-2.30 |1.59 |NA |

Relative expression ratio of target samples:

|ID |Roche Method |Pfaffl Method |delta delta Cq Method | |:------|:------------|:-------------|:---------------------| |23 |-199.269 |-118.1844 |10.64 | |32 |8.714 |-3.0624 |-1.67 | |74 |-0.713 |0.4215 |13.13 | |86 |-2.757 |-0.9171 |13.84 | |91 |-1.929 |-0.0885 |1.34 | |94 |-1.218 |-0.0731 |-2.39 | |95 |-0.463 |-0.2580 |-1.60 |

Settings used during RT-qPCR analysis:

Select the type of PCR: LC480

Select efficiency computing method: sigfit

Select to apply the cut off: None

Cq cut off: NA

efficiency cut off: NA

Select to replace the specific Cq and Eff. values: None

The row, where Cq value is to be replaced:

New Cq value:

The row, where efficiency value is to be replaced: NA

New Efficiency value: NA

Select to replace all NAs by user defined value: None

Provide the Cq value to replace NAs: NA

Provide the efficiency value to replace NAs: NA

Select method to remove nondetects: None

Select method to combine Technical Replicates: Mean

Type the name of reference gene under column 'Target Name': hk

Session Information:

R version 3.3.2 (2016-10-31) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252

attached base packages: character(0)

other attached packages: [1] RTqPCR_1.0

loaded via a namespace (and not attached): [1] Rcpp_0.12.9 BiocInstaller_1.24.0 DEoptimR_1.0-8 [4] RColorBrewer_1.1-2 NormqPCR_1.20.0 ReadqPCR_1.20.0 [7] highr_0.6 methods_3.3.2 utils_3.3.2 [10] tools_3.3.2 grDevices_3.3.2 zlibbioc_1.20.0 [13] digest_0.6.12 jsonlite_1.3 evaluate_0.10 [16] preprocessCore_1.36.0 lattice_0.20-34 Matrix_1.2-7.1 [19] shiny_1.0.3 parallel_3.3.2 stringr_1.2.0 [22] knitr_1.15.1 graphics_3.3.2 htmlwidgets_0.8 [25] datasets_3.3.2 stats_3.3.2 sourcetools_0.1.5 [28] rprojroot_1.2 grid_3.3.2 robustbase_0.92-7 [31] base_3.3.2 Biobase_2.34.0 R6_2.2.0 [34] rgl_0.97.0 minpack.lm_1.2-1 rmarkdown_1.5 [37] qpcR_1.4-0 magrittr_1.5 backports_1.0.5 [40] htmltools_0.3.5 MASS_7.3-45 BiocGenerics_0.20.0 [43] mime_0.5 xtable_1.8-2 httpuv_1.3.3 [46] stringi_1.1.2 affy_1.52.0 markdown_0.7.7 [49] affyio_1.44.0

NPhogat/RTqPCR documentation built on July 12, 2020, 12:56 p.m.