User: Chaimaa

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Chaimaa160
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Posts by Chaimaa

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how to get Cinical drug response data from broad GDAC firehose?
... hi guys, Could anyone guide me on how to get clinical drug response data from TCGA ? I have access to the broad GDAC firehose website [GDAC data][1] and download a "Clinical_Pick_Tier1 (MD5)" of some cancer types ,Unfortunately, i found no informations about drugs, and if even exist are all "NA". ...
drugs written 5 days ago by Chaimaa160 • updated 4 days ago by Kevin Blighe54k
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Comment: C: what is the ideal normalistation methods for TCGA gene expression or DNA methyla
... this is the gene expression file looks like after the download https://postimg.cc/nsymVY8Q and here is the DNA methylation looks like https://postimg.cc/MfWmxbRm ...
written 5 weeks ago by Chaimaa160
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Comment: C: what is the ideal normalistation methods for TCGA gene expression or DNA methyla
... ok @genomax from this website i access and get my data http://firebrowse.org/?cohort=COADREAD&download_dialog=true ...
written 5 weeks ago by Chaimaa160
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Comment: C: what is the ideal normalistation methods for TCGA gene expression or DNA methyla
... @ATpoint ok i will share the original files of them here, is it ok? ...
written 5 weeks ago by Chaimaa160
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Comment: C: what is the ideal normalistation methods for TCGA gene expression or DNA methyla
... is there any normalization steps can be applied directly on these data, if anyone experts in this issue plz guide me through? ...
written 5 weeks ago by Chaimaa160
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Comment: C: what is the ideal normalistation methods for TCGA gene expression or DNA methyla
... @ATpoint Hi, when i downloaded these data from Broad Firehose, i choose only the preprocessed files. For gene expression i take this file (mRNA_Preprocess_Median (MD5)) and for DNA methylation i take this file (Methylation_Preprocess (MD5)) then i integrated them together for the same set of sample ...
written 5 weeks ago by Chaimaa160
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Comment: C: what is the ideal normalistation methods for TCGA gene expression or DNA methyla
... @ATpoint yes, this is the raw data i have, no there is no TPM transformation , this all what i have ...
written 6 weeks ago by Chaimaa160
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Comment: C: what is the ideal normalistation methods for TCGA gene expression or DNA methyla
... @ATpoint below i have explain for you what i got and what i have tried. ...
written 6 weeks ago by Chaimaa160
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Comment: C: what is the ideal normalistation methods for TCGA gene expression or DNA methyla
... @ATpoint, Hi, here are my data looks like, rows represente samples and columns represent list of genes and the values inside the cells indicate the expression and methylation values as i got from Broad website. So these values as i think are not normalized enough to be used for any further analysis ...
written 6 weeks ago by Chaimaa160 • updated 6 weeks ago by ATpoint29k
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Comment: C: what is the ideal normalistation methods for TCGA gene expression or DNA methyla
... @ok i will provide some of the row and columns from these data here, Note that these data i got from gdac broad institute Firehose ...
written 6 weeks ago by Chaimaa160

Latest awards to Chaimaa

Great Question 7 weeks ago, created a question with more than 5,000 views. For How to extract the list of genes from TCGA CNV data
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Popular Question 11 months ago, created a question with more than 1,000 views. For how to link list of genes using PPI networks?
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