# Talk:20.109(S13):Transcript-level analysis (Day6)

(Difference between revisions)
 Revision as of 11:01, 3 May 2013 (view source) (→Cross-group meetings)← Previous diff Current revision (08:45, 8 May 2013) (view source) (→W/F) (6 intermediate revisions not shown.) Line 3: Line 3: ===T/R=== ===T/R=== - The text file below contains all of the T/R data. Two different CP values are given. The first is calculated when all samples are thresholded at the same level. The second is calculated when a separate threshold is made for each primer set. (T/R Purple, because your samples ran separately, there were not enough of them to make a per RNA threshold reasonable.) + The Excel file below contains all of the T/R data. Two different CP values are given. The first is calculated when all samples are thresholded at the same level. The second is calculated when a separate threshold is made for each primer set. (T/R Purple, because your samples ran separately, there were not enough of them to make a per RNA threshold reasonable.) - [[Media:20109-S13_TR_qPCR.txt]] + [[Media:20109-S13_TR_qPCR.xlsx]] ===W/F=== ===W/F=== - The text file below contains all of the T/R data. Two different CP values are given. The first is calculated when all samples are thresholded at the same level. The second is calculated when a separate threshold is made for each primer set. + The Excel file below contains all of the T/R data. Two different CP values are given. The first is calculated when all samples are thresholded at the same level. The second is calculated when a separate threshold is made for each primer set. - [[Media:20109-S13_WF_qPCR.txt]] + [[Media:20109-S13_WF_qPCR.xlsx]] ==qPCR section-wide curves== ==qPCR section-wide curves== + + ===T/R=== [[Image:S13_M3D5_TR_raw.jpg|thumb|400px|left|T/R section, Raw amplification curves]] [[Image:S13_M3D5_TR_raw.jpg|thumb|400px|left|T/R section, Raw amplification curves]] [[Image:S13_M3D5_TR_noiseband.jpg|thumb|400px|center|T/R section, Log-scale amplification curves with noise threshold]] [[Image:S13_M3D5_TR_noiseband.jpg|thumb|400px|center|T/R section, Log-scale amplification curves with noise threshold]] - [[Image:S13_M3D5_TR_18S-melt.jpg|thumb|300px|right|T/R section, Melt curves for 18 samples]] + [[Image:S13_M3D5_TR_18S-melt.jpg|thumb|300px|right|T/R section, Melt curves for 18S samples]] [[Image:S13_M3D5_TR_CNII-melt.jpg|thumb|300px|left|T/R section, Melt curves for CN II samples]] [[Image:S13_M3D5_TR_CNII-melt.jpg|thumb|300px|left|T/R section, Melt curves for CN II samples]] [[Image:S13_M3D5_TR_CNI-melt.jpg|thumb|300px|center|T/R section, Melt curves for CN II samples]] [[Image:S13_M3D5_TR_CNI-melt.jpg|thumb|300px|center|T/R section, Melt curves for CN II samples]] + + [[Image:S13_M3D5_TR_18S-noiseband.jpg|thumb|300px|right|T/R section, Amp curves for 18S samples]] + [[Image:S13_M3D5_TR_CNII-noiseband.jpg|thumb|300px|left|T/R section, Amp curves for CN II samples]] + [[Image:S13_M3D5_TR_CNI-noiseband.jpg|thumb|300px|center|T/R section, Amp curves for CN II samples]] +

+ ===W/F=== [[Image:S13_M3D5_WF_raw.jpg|thumb|400px|left|W/F section, Raw amplification curves]] [[Image:S13_M3D5_WF_raw.jpg|thumb|400px|left|W/F section, Raw amplification curves]] Line 30: Line 38: [[Image:S13_M3D5_WF_CNII-melt.jpg|thumb|300px|left|W/F section, Melt curves for CN II samples]] [[Image:S13_M3D5_WF_CNII-melt.jpg|thumb|300px|left|W/F section, Melt curves for CN II samples]] [[Image:S13_M3D5_WF_CNI-melt.jpg|thumb|300px|center|W/F section, Melt curves for CN II samples]] [[Image:S13_M3D5_WF_CNI-melt.jpg|thumb|300px|center|W/F section, Melt curves for CN II samples]] + + [[Image:S13_M3D5_WF_18S-noiseband.jpg|thumb|300px|right|W/F section, Amp curves for 18S samples]] + [[Image:S13_M3D5_WF_CNII-noiseband.jpg|thumb|300px|left|W/F section, Amp curves for CN II samples]] + [[Image:S13_M3D5_WF_CNI-noiseband.jpg|thumb|300px|center|W/F section, Amp curves for CN II samples]] + +
==Cross-group meetings== ==Cross-group meetings== Line 50: Line 64: ===W/F Scheme=== ===W/F Scheme=== + Blue 1/Platinum 2 + *Emmanuel/Shanthi + + + Blue 2/Green 2 + *Divya/Steve + + + Green 1/Platinum 1 + *Kevin/Eric + + + Yellow 1/Orange 2 + *Karinna/Katie + + + Pink 2/Purple 1 + *Alice/Zeinab + + + Purple 2/Orange 1 + *Jenny V./Ameila + + + Yellow 2/Pink 1 + *Jenny W./Helen

## qPCR data

### T/R

The Excel file below contains all of the T/R data. Two different CP values are given. The first is calculated when all samples are thresholded at the same level. The second is calculated when a separate threshold is made for each primer set. (T/R Purple, because your samples ran separately, there were not enough of them to make a per RNA threshold reasonable.)

### W/F

The Excel file below contains all of the T/R data. Two different CP values are given. The first is calculated when all samples are thresholded at the same level. The second is calculated when a separate threshold is made for each primer set.

## qPCR section-wide curves

### T/R

T/R section, Raw amplification curves
T/R section, Log-scale amplification curves with noise threshold
T/R section, Melt curves for 18S samples
T/R section, Melt curves for CN II samples
T/R section, Melt curves for CN II samples
T/R section, Amp curves for 18S samples
T/R section, Amp curves for CN II samples
T/R section, Amp curves for CN II samples

### W/F

W/F section, Raw amplification curves
W/F section, Log-scale amplification curves with noise threshold
W/F section, Melt curves for 18 samples
W/F section, Melt curves for CN II samples
W/F section, Melt curves for CN II samples
W/F section, Amp curves for 18S samples
W/F section, Amp curves for CN II samples
W/F section, Amp curves for CN II samples

## Cross-group meetings

### T/R Scheme

Red 1/Yellow 1: Marisol/Dominique

Red 2/Blue 1: Nick/Justin

Orange 1/Platinum 2: Daphne/Katie

Platinum 1/Blue 2: Emily/Noa

Yellow 2/Green 2: Ebaa/Jesse

Green 1/Purple 1:Nikki/Sarah

Orange 2/Purple 2: Stas/Mitali

### W/F Scheme

Blue 1/Platinum 2

• Emmanuel/Shanthi

Blue 2/Green 2

• Divya/Steve

Green 1/Platinum 1

• Kevin/Eric

Yellow 1/Orange 2

• Karinna/Katie

Pink 2/Purple 1

• Alice/Zeinab

Purple 2/Orange 1

• Jenny V./Ameila

Yellow 2/Pink 1

• Jenny W./Helen