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Saturday, September 15

Tuesday, September 4

  1. page Hanie's lab notebook 2 edited ... Abstract 2018-09-04 ... I modified code/Habil/AML/dnam/read.TCGA and used code/Habil/AM…
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    Abstract
    2018-09-04
    ...
    I modified code/Habil/AML/dnam/read.TCGA and used code/Habil/AML/dnam/read.TCGAit to read
    ...
    of downloaded datasetsdatasets, separately. The resultsIt created an RData object which consists of a matrix of DNA methylation values. Rows of this matrix are DNA loci and columns are clinical samples.
    The values of these two matrix
    are the
    2018-08-30
    Based on reading the below mentioned paper, RnBeads vignette, tutorial and final report, I found that I should use the methylumi package. Based on the final report {2018-08-31_RnBeads_report.zip} of the RnBeads: normalization.method="swan"
    (view changes)
    11:28 am
  2. page Hanie's lab notebook 2 edited ... Thesis presentation Abstract 2018-09-04 I downloaded DNA methylation data from the TCGA po…
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    Thesis presentation
    Abstract
    2018-09-04
    I downloaded DNA methylation data from the TCGA portal using 1) TCGA data portal downloader 2) code/Ghazal/iNetgrator/download.data. I modified and used code/Habil/AML/dnam/read.TCGA to read DNA methylation files of each sample for each of downloaded datasets separately. The results are the same. However, these results are different from our original results that we used DNA methylation data downloaded from the TCGA website. There are 54 samples {2018-09-04_omited_TCGA_DNAm_Samples.csv} removed from the TCGA data portal.

    2018-08-30
    Based on reading the below mentioned paper, RnBeads vignette, tutorial and final report, I found that I should use the methylumi package. Based on the final report {2018-08-31_RnBeads_report.zip} of the RnBeads: normalization.method="swan"
    (view changes)
    11:16 am

Thursday, August 30

  1. page Hanie's lab notebook 2 edited ... Abstract 2018-08-30 ... on reading thebelow the below mentioned paper, RnBeadsvigneete…
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    Abstract
    2018-08-30
    ...
    on reading thebelowthe below mentioned paper, RnBeadsvigneete,RnBeads vignette, tutorial and
    ...
    should use themethylumithe methylumi package. Based
    normalization.background.method= "methylumi.noob"
    2018-08-29
    (view changes)
    10:53 pm
  2. page Hanie's lab notebook 2 edited ... Thesis presentation Abstract 2018-08-30 Based on reading thebelow mentioned paper, RnBeads…
    ...
    Thesis presentation
    Abstract
    2018-08-30
    Based on reading thebelow mentioned paper, RnBeadsvigneete, tutorial and final report, I found that I should use themethylumi package. Based on the final report {2018-08-31_RnBeads_report.zip} of the RnBeads: normalization.method="swan"
    normalization.background.method= "methylumi.noob"

    2018-08-29
    DNAm packages [1 , 2]
    (view changes)
    10:52 pm

Wednesday, August 29

  1. page Hanie's lab notebook 2 edited ... DNAm packages [1 , 2] comparison between some of DNAm packages >>MIAME (Minimum Info…
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    DNAm packages [1 , 2]
    comparison between some of DNAm packages
    >>MIAME (Minimum Information about a Microarray Experiment)
    shinymethyl and methylumi are not proper choices.
    minfi
    (view changes)
    6:08 pm
  2. page Hanie's lab notebook 2 edited ... Abstract 2018-08-29 DNAm packages. packages [1 , 2] comparison between some of DNAm pack…
    ...
    Abstract
    2018-08-29
    DNAm packages.packages [1 , 2]
    comparison between some of DNAm packages

    shinymethyl and methylumi are not proper choices.
    minfi
    (view changes)
    6:06 pm

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