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  • Beta density distribution across samples

    Uploaded by

    Alfonso Peñarroya
    9 views19 pages
    The document contains plots showing the density distribution of beta values for various samples labeled P96 to P08. Scatter plots also show log intensity values for these same samples labeled on the x-axis across two conditions of a bisulfite conversion experiment.

    Original Description:

    Methylation array report

    Original Title

    Qc Report

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    © © All Rights Reserved

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    The document contains plots showing the density distribution of beta values for various samples labeled P96 to P08. Scatter plots also show log intensity values for these same samples labeled on the x-axis across two conditions of a bisulfite conversion experiment.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Flag for inappropriate content
    9 views19 pages

    Beta density distribution across samples

    Uploaded by

    Alfonso Peñarroya
    The document contains plots showing the density distribution of beta values for various samples labeled P96 to P08. Scatter plots also show log intensity values for these same samples labeled on the x-axis across two conditions of a bisulfite conversion experiment.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Flag for inappropriate content
    of 19

    Beta

    5
    4
    3
    Density

    2
    1
    0

    0.0 0.2 0.4 0.6 0.8 1.0

    Beta
    Beta

    P96

    P95

    P94

    P83

    P75

    P72

    P68

    P60

    P54

    P409

    P401

    P395

    P387

    P379

    P377

    P373

    P367

    0.0 0.2 0.4 0.6 0.8 1.0

    Beta
    Beta

    P365

    P317

    P305

    P269

    P267

    P26

    P205

    P193

    P189

    P183

    P163

    P162

    P161

    P158

    P132

    P08

    0.0 0.2 0.4 0.6 0.8 1.0

    Beta
    Control: BISULFITE CONVERSION I
    6 8 10 12 14 16

    Red Green

    P96 ●
    ●●● ●● ● ●● ●
    ● ● ●● ● ● ●●

    P95 ●
    ●
    ●● ● ● ●●
    ● ●
    ●● ●●
    ●● ● ●●

    P94 ●●●
    ● ●● ● ●●● ● ●●● ●●
    ● ● ●●

    P83 ●●
    ●● ●● ● ●●
    ● ● ● ● ●●
    ●● ● ●●

    P75 ●●● ●● ● ● ●●
    ● ●●
    ● ●●
    ●● ● ●●

    P72 ●●●● ●
    ● ● ●
    ●
    ● ●●
    ● ●●
    ● ● ● ●●

    P68 ● ●●● ●● ● ●● ●●
    ● ● ●● ● ●●

    P60 ●●●
    ● ●● ● ●●
    ● ●● ●
    ● ●●
    ● ● ●
    ●
    sample

    P54 ●●● ●● ● ●●
    ● ● ●
    ● ● ●
    ●● ● ●●

    P409 ●●
    ●● ●● ● ●●
    ● ●
    ●● ●● ●
    ● ● ●●

    P401 ●●
    ●● ●● ● ●
    ● ●● ● ●●
    ● ● ● ●●

    P395 ●●
    ● ● ●● ● ●● ●
    ●● ●
    ●●● ● ●●

    P387 ●●●● ●● ● ●●
    ● ● ●● ● ●●● ● ●●

    P379 ●
    ● ● ●
    ● ● ●●
    ● ● ●
    ● ● ● ●● ● ●●

    P377 ●
    ●● ●●● ● ●●
    ● ●●● ●
    ● ● ● ● ●●

    P373 ●●● ● ● ● ●●
    ● ●●●
    ● ●● ● ●●

    P367 ● ●● ● ●● ● ●●
    ● ●
    ●● ●
    ●● ● ●●

    6 8 10 12 14 16

    Log2 Intensity
    Control: BISULFITE CONVERSION I
    6 8 10 12 14 16

    Red Green

    P365 ●● ● ●● ● ●●
    ● ● ●● ● ●
    ● ● ●●

    P317 ●●
    ● ●● ● ●●
    ● ● ● ● ● ●●
    ● ● ●●

    P305 ● ●●● ●
    ● ● ●●
    ● ●● ● ●● ● ● ●●

    P269 ●●● ●● ● ● ●●
    ● ● ●● ● ●●
    ● ● ●●

    P267 ●●
    ●
    ● ● ● ●●
    ● ● ●●● ●●
    ● ● ●●

    P26 ●●● ● ● ● ● ●● ●●● ●●● ● ● ●●

    P205 ●●● ●● ● ●
    ●● ●● ● ●● ●● ● ●●

    P193 ●●
    ●● ●● ● ●●
    ● ●●● ● ●●● ● ●●
    sample

    P189 ●●●● ●● ● ●● ●● ●
    ●● ● ● ●●

    P183 ●
    ●●
    ● ● ● ●● ●● ● ● ● ● ● ●●

    P163 ●
    ●● ●● ● ● ●●
    ● ●●●● ●
    ● ● ●●

    P162 ●●●● ●
    ● ● ●● ●●● ● ●
    ●● ● ●●

    P161 ● ● ● ●
    ● ● ●
    ●● ● ● ●● ● ● ●●

    P158 ● ●●● ●● ● ●● ● ●
    ●● ● ● ● ●●

    P132 ●●●● ●● ● ●● ● ● ●● ● ● ●●

    P08 ●●
    ●● ●● ● ●●
    ● ●● ●●● ● ● ●●

    6 8 10 12 14 16

    Log2 Intensity
    Control: BISULFITE CONVERSION II
    6 8 10 12 14 16

    Red Green

    P96 ● ●●
    ● ● ● ● ●

    P95 ● ●●● ● ● ● ●

    P94 ● ●● ●● ● ●

    P83 ● ●●
    ● ●● ● ●

    P75 ● ●● ● ● ● ●

    P72 ● ●●● ● ● ● ●

    P68 ● ●●
    ● ● ● ● ●

    P60 ● ●●
    ● ●● ● ●
    sample

    P54 ● ●● ●
    ● ● ●

    P409 ● ●● ●● ● ●

    P401 ● ●●
    ● ●● ● ●

    P395 ● ●●
    ● ●● ● ●

    P387 ● ●●● ●● ● ●

    P379 ● ●●
    ● ●● ●●

    P377 ● ●●
    ● ●● ● ●

    P373 ● ●● ● ● ● ●

    P367 ● ●●
    ● ●● ● ●

    6 8 10 12 14 16

    Log2 Intensity
    Control: BISULFITE CONVERSION II
    6 8 10 12 14 16

    Red Green

    P365 ● ● ●● ●● ● ●

    P317 ● ●●● ●● ● ●

    P305 ● ●●
    ● ●● ● ●

    P269 ● ●● ● ● ● ●

    P267 ● ●●
    ● ● ● ●

    P26 ● ●●● ●● ● ●

    P205 ● ●●
    ● ●● ●●

    P193 ● ●●
    ● ●● ● ●
    sample

    P189 ● ●●
    ● ● ● ● ●

    P183 ● ●●
    ● ●● ●●

    P163 ● ●●
    ● ●
    ● ●●

    P162 ● ●● ● ● ● ●

    P161 ● ●●
    ● ●
    ● ● ●

    P158 ● ●●
    ● ●● ● ●

    P132 ● ●●● ●● ● ●

    P08 ● ●●
    ● ● ● ●

    6 8 10 12 14 16

    Log2 Intensity
    Control: EXTENSION
    6 8 10 12 14 16

    Red Green

    P96 ● ● ● ● ● ●●

    P95 ●
    ● ● ●● ●●

    P94 ● ●
    ● ● ● ●●

    P83 ● ● ● ●
    ● ●●

    P75 ●
    ● ●
    ● ● ● ●●

    P72 ●● ●
    ● ● ● ●●

    P68 ● ● ●
    ● ● ● ●●

    P60 ●
    ● ●
    ● ●● ●●
    sample

    P54 ● ● ● ●● ●●

    P409 ●● ●
    ● ● ● ●●

    P401 ●● ●
    ● ●● ●●

    P395 ●● ● ● ● ●●

    P387 ● ●
    ● ● ● ●●

    P379 ●● ●
    ● ● ●●

    P377 ●
    ● ● ●● ●●

    P373 ● ● ●
    ● ●●

    P367 ● ● ● ●● ●●

    6 8 10 12 14 16

    Log2 Intensity
    Control: EXTENSION
    6 8 10 12 14 16

    Red Green

    P365 ●● ● ●● ●●

    P317 ●
    ● ● ● ● ●●

    P305 ● ● ●
    ● ● ● ●●

    P269 ●● ●
    ● ● ● ●●

    P267 ● ●
    ● ●● ●●

    P26 ●
    ● ●
    ● ●● ●●

    P205 ●
    ● ● ●● ●●

    P193 ● ● ● ● ● ●●
    sample

    P189 ● ● ●● ●●

    P183 ● ● ● ● ● ●●

    P163 ●
    ● ●
    ● ●● ●●

    P162 ● ● ● ● ●●

    P161 ● ● ● ● ● ●●

    P158 ● ●
    ● ● ● ●●

    P132 ● ● ●
    ● ●● ●●

    P08 ●
    ● ●
    ● ●● ●●

    6 8 10 12 14 16

    Log2 Intensity
    Control: HYBRIDIZATION
    6 8 10 12 14 16

    Red Green

    P96 ● ● ● ● ● ●

    P95 ● ● ● ● ● ●

    P94 ● ● ● ● ● ●

    P83 ● ● ● ● ● ●

    P75 ● ● ● ● ● ●

    P72 ● ● ● ● ● ●

    P68 ● ● ● ● ● ●

    P60 ● ● ● ● ● ●
    sample

    P54 ● ● ● ● ● ●

    P409 ● ● ● ● ● ●

    P401 ● ● ● ● ● ●

    P395 ● ● ● ● ● ●

    P387 ● ● ● ● ● ●

    P379 ● ● ● ● ● ●

    P377 ● ● ● ● ● ●

    P373 ● ● ● ● ● ●

    P367 ● ● ● ● ● ●

    6 8 10 12 14 16

    Log2 Intensity
    Control: HYBRIDIZATION
    6 8 10 12 14 16

    Red Green

    P365 ● ● ● ● ● ●

    P317 ● ● ● ● ● ●

    P305 ● ● ● ● ● ●

    P269 ● ● ● ● ● ●

    P267 ● ● ● ● ● ●

    P26 ● ● ● ● ● ●

    P205 ● ● ● ● ● ●

    P193 ● ● ● ● ● ●
    sample

    P189 ● ● ● ● ● ●

    P183 ● ● ● ● ● ●

    P163 ● ● ● ● ● ●

    P162 ● ● ● ● ● ●

    P161 ● ● ● ● ● ●

    P158 ● ● ● ● ● ●

    P132 ● ● ● ● ● ●

    P08 ● ● ● ● ● ●

    6 8 10 12 14 16

    Log2 Intensity
    Control: NON−POLYMORPHIC
    6 8 10 12 14 16

    Red Green

    P96 ●●● ● ●● ●● ● ●
    ● ●● ●

    P95 ●●●
    ●●●● ●● ● ●
    ●● ●

    P94 ● ●●
    ● ●●
    ● ●● ●●
    ●● ●● ●●

    P83 ● ●●● ●● ● ●● ● ●● ● ● ●●

    P75 ● ●●●●● ●● ● ●●
    ●●
    ●● ●
    ●

    P72 ●●
    ● ● ●● ● ●●
    ●● ● ● ●
    ●

    P68 ●● ● ●●● ●● ● ●
    ●●
    ● ●● ●
    ●

    P60 ●●
    ●● ●●
    ● ●● ●●●● ●● ●
    sample

    P54 ●
    ● ●
    ● ●● ●● ● ●●
    ● ●● ●
    ●

    P409 ●● ●● ●● ●● ● ●●
    ● ●● ●
    ●

    P401 ●
    ●● ●
    ● ●● ●●●●
    ● ● ● ●
    ●

    P395 ●● ●● ●●
    ● ● ● ●●
    ●● ●
    ● ●

    P387 ● ● ●●
    ●● ●● ● ●
    ●● ● ● ●

    P379 ●
    ●●● ● ●
    ● ●● ●● ●●
    ● ●● ●●

    P377 ●
    ● ●● ●
    ● ● ●● ● ● ●

    P373 ●●● ●● ●● ●●● ●● ●


    ●

    P367 ●●● ●●
    ● ●● ●●●●● ●● ●
    ●

    6 8 10 12 14 16

    Log2 Intensity
    Control: NON−POLYMORPHIC
    6 8 10 12 14 16

    Red Green

    P365 ● ●●● ● ● ● ●● ● ●●●


    ● ●
    ● ●
    ●

    P317 ●
    ●● ●●● ●
    ● ● ●
    ●●●
    ● ●
    ●

    P305 ●●●
    ● ●●● ●● ●●●● ● ● ●
    ●

    P269 ●●●● ●
    ●
    ● ●● ● ● ●●● ● ● ●
    ●

    P267 ●
    ●
    ● ●●
    ● ●
    ● ●● ●
    ●● ● ● ●
    ●

    P26 ●
    ●
    ●● ● ●● ● ●●
    ●● ● ●
    ●

    P205 ●●
    ● ●●● ●● ● ●●● ●● ●
    ●

    P193 ●●
    ●● ● ● ● ●
    ● ●●●●
    ● ●● ●
    ●
    sample

    P189 ●●
    ●●●● ●● ●●●● ● ● ●

    P183 ●● ● ●
    ●●● ●● ● ●●
    ●● ●● ●
    ●

    P163 ● ●●● ●●● ●● ● ●●


    ●● ●● ●
    ●

    P162 ●●
    ●●● ● ●● ●● ●
    ● ● ● ●
    ●

    P161 ● ●●
    ● ●
    ●● ●
    ● ●●●
    ●● ●
    ● ●
    ●

    P158 ●●● ● ●● ●● ● ●
    ●
    ●● ●● ●
    ●

    P132 ●● ● ●●● ●● ●
    ●
    ● ●● ●
    ●

    P08 ●●
    ●● ● ●● ●● ●●●
    ●●● ●●

    6 8 10 12 14 16

    Log2 Intensity
    Control: SPECIFICITY I
    6 8 10 12 14 16

    Red Green

    P96 ● ● ●●●●● ● ● ● ● ● ● ● ●●
    ●● ●● ● ● ●

    P95 ● ●
    ●● ●● ● ● ● ●● ●
    ● ●● ●● ● ● ●

    P94 ● ●●
    ●●●● ● ● ● ● ●●
    ●
    ●●●
    ●● ● ● ●

    P83 ●●● ●● ●● ● ● ● ●● ● ● ●●● ●● ● ● ●

    P75 ● ●●
    ●●● ● ● ● ●● ●●●
    ●●●● ● ● ● ●

    P72 ●
    ●● ●●●
    ● ● ● ●● ● ●
    ●
    ●●●● ●
    ● ● ● ●

    P68 ● ●●● ●●
    ●● ● ● ●● ●
    ●
    ●●● ●
    ● ●● ● ● ●

    P60 ● ●
    ●●● ●
    ●
    ● ● ● ● ● ● ● ●●
    ●● ●● ● ● ●
    sample

    P54 ●
    ● ●● ●●
    ● ● ● ●● ●●●
    ●
    ● ●● ● ● ●

    P409 ● ●●
    ●● ●●● ● ● ●● ●
    ●●
    ●●●
    ● ●● ● ● ●

    P401 ● ●●●● ●● ● ● ●● ●●
    ●●●
    ●● ●● ● ● ●

    P395 ● ● ● ●● ● ● ●● ● ●●
    ●●● ● ● ● ● ●

    P387 ● ● ●● ●● ● ● ● ●● ●●
    ●●●
    ● ●● ● ● ●

    P379 ● ● ● ●● ●● ● ● ● ● ●● ●
    ●●● ●
    ● ● ● ●

    P377 ●● ● ●● ●● ● ● ●● ●●
    ●●
    ●
    ●● ●● ● ● ●

    P373 ● ●●
    ●●●● ● ● ● ●● ●
    ●●● ●
    ● ● ● ●

    P367 ●● ●● ●
    ●●● ● ● ●● ●
    ●●●● ● ●● ● ● ●

    6 8 10 12 14 16

    Log2 Intensity
    Control: SPECIFICITY I
    6 8 10 12 14 16

    Red Green

    P365 ● ●
    ●●●●●
    ● ● ● ●● ●
    ●●● ● ●● ● ● ● ●

    P317 ●●● ●●● ● ● ● ●● ● ●


    ●●●
    ● ●
    ● ● ● ●

    P305 ● ●●● ●●● ● ● ● ●● ●


    ●●● ●
    ● ●
    ● ● ● ●

    P269 ●
    ●●●● ●●
    ● ● ● ●● ●●
    ●●● ●● ● ● ●

    P267 ● ●● ●● ● ● ●● ● ●●
    ●
    ●● ●● ● ● ●

    P26 ● ●● ●●●● ● ● ●● ● ● ●●
    ●● ● ●● ● ● ●

    P205 ●● ●●
    ● ●● ● ● ●● ● ●●
    ●
    ● ● ●● ● ● ●

    P193 ● ●●
    ● ●●
    ●● ● ● ● ● ●
    ●
    ●● ●
    ●● ● ● ●
    sample

    P189 ● ●
    ●
    ●● ●
    ●● ● ● ●● ●●●
    ● ●●● ● ● ●

    P183 ● ● ● ●● ● ● ● ●● ●●
    ●
    ●●● ●
    ● ● ● ●

    P163 ●●
    ●●● ●● ● ● ● ● ● ● ●●●● ●●● ● ● ●

    P162 ● ●
    ● ●●●
    ● ● ● ●● ●
    ●●
    ●●● ● ●● ● ● ●

    P161 ●●●●●
    ● ●● ● ● ●● ●
    ●●●● ●
    ● ● ● ●

    P158 ● ●● ●● ●
    ●● ● ● ●● ●● ● ● ●
    ● ●● ● ● ●

    P132 ●● ●● ● ●
    ●● ● ● ●● ●●●● ●●
    ●
    ● ● ● ● ●

    P08 ● ●●
    ●
    ● ●●● ● ● ● ● ●●●●
    ● ● ● ● ● ●

    6 8 10 12 14 16

    Log2 Intensity
    Control: SPECIFICITY II
    6 8 10 12 14 16

    Red Green

    P96 ●●● ● ●

    P95 ●●● ●
    ● ●

    P94 ●
    ●● ●●

    P83 ●●● ●● ●

    P75 ●● ● ●● ●

    P72 ●●● ● ● ●

    P68 ●●● ● ●●

    P60 ●
    ●● ● ●
    sample

    P54 ●●● ●●●

    P409 ●●● ● ●●

    P401 ●● ● ●● ●

    P395 ●●● ● ●●

    P387 ●●● ● ●●

    P379 ●●● ● ●

    P377 ●●● ● ●●

    P373 ●● ● ●
    ●●

    P367 ●●● ●●●

    6 8 10 12 14 16

    Log2 Intensity
    Control: SPECIFICITY II
    6 8 10 12 14 16

    Red Green

    P365 ●● ● ● ●●

    P317 ●● ● ●● ●

    P305 ●● ● ●
    ●●

    P269 ●●● ●●●

    P267 ●●● ●●●

    P26 ●●● ● ●

    P205 ●●● ●
    ●●

    P193 ●●● ●●●


    sample

    P189 ●●● ●
    ●●

    P183 ●●● ●
    ●●

    P163 ●●● ● ●●

    P162 ●●● ●● ●

    P161 ●●● ● ●

    P158 ●●● ●●

    P132 ●●● ●●●

    P08 ●●● ●●●

    6 8 10 12 14 16

    Log2 Intensity
    Control: TARGET REMOVAL
    6 8 10 12 14 16

    Red Green

    P96 ●● ● ●

    P95 ●
    ● ● ●

    P94 ●● ●●

    P83 ●
    ● ● ●

    P75 ●
    ● ● ●

    P72 ● ● ●

    P68 ●● ● ●

    P60 ● ● ●●
    sample

    P54 ●● ● ●

    P409 ●● ● ●

    P401 ●● ● ●

    P395 ●● ● ●

    P387 ●● ● ●

    P379 ●● ●●

    P377 ●
    ● ● ●

    P373 ● ●●

    P367 ●
    ● ● ●

    6 8 10 12 14 16

    Log2 Intensity
    Control: TARGET REMOVAL
    6 8 10 12 14 16

    Red Green

    P365 ●● ● ●

    P317 ●
    ● ●●

    P305 ● ● ● ●

    P269 ● ● ● ●

    P267 ● ● ●

    P26 ●● ● ●

    P205 ●● ● ●

    P193 ●● ● ●
    sample

    P189 ●● ●●

    P183 ●● ● ●

    P163 ●● ●●

    P162 ●● ● ●

    P161 ●
    ● ● ●

    P158 ●● ● ●

    P132 ● ● ●●

    P08 ●● ●●

    6 8 10 12 14 16

    Log2 Intensity

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