User: english.server

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Posts by english.server

<prev • 88 results • page 1 of 9 • next >
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Inconsistent survival times in TCGA clinicalMatrix file?
... While trying to anaylze survival of glioblastoma patients, I came up with the following data from downloaded GBM_clinicalMatrix file: sampleID CDE_survival_time CDE_vital_status days_to_last_followup TCGA.06.5859.01 138 LIVING 139 TCGA.27.1831.01 ...
tcga data survival analysis written 8 hours ago by english.server210 • updated 1 hour ago by Kevin Blighe63k
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Comment: C: Too many RNAseq samples. What to do?
... Thanks. That would be of great advantage if I could compute the amount of RAM for my work. I am going to compare whithin TCGA DEGs and TCGA vs GTEx DEGs; ie once compare cancerous vs normal tissue present in TCGA data and then the TCGA cancerous tissue with GTEX. For the batch effects, no actually ...
written 5 days ago by english.server210
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Comment: C: Too many RNAseq samples. What to do?
... Thanks. I updated the post. ...
written 5 days ago by english.server210
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Too many RNAseq samples. What to do?
... Dear Biostarsers! I wanted to obtain TCGA vs GTex differentially expressed genes using either DESEQ2 or EdgeR; however, I cannot use Amazon and Galaxy failed to do the job, and the amount of RAM on my laptop didnt allow the computation. I thought using non-bayesian techniques might solve my problem ...
deseq2 rna-seq edger written 5 days ago by english.server210
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Comment: C: Differential gene expression, starting from RSEM expected count values.
... Thank you. especially useful answer as the other post/point of view I referred to is answered by you. Thanks ...
written 5 months ago by english.server210
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Differential gene expression, starting from RSEM expected count values.
... Hi! I could/should have asked this question at bioC forum, but the answers there are usually (just) over my head. I wondered how to use a table of "Expected counts" from rsem to obtain DEGs using DeSeq2/EdgeR? The expected counts are from UCSC Xena- processed GTEX data. There seems to be more ...
expected-count deseq2 rsem written 5 months ago by english.server210 • updated 5 months ago by i.sudbery8.4k
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Comment: C: Survival analysis: Why to categorize age?
... Thank you. Valuable information. ...
written 6 months ago by english.server210
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Comment: C: Survival analysis: Why to categorize age?
... Useful link. Thanks a lot ...
written 6 months ago by english.server210
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Comment: C: Survival analysis: Why to categorize age?
... This was my "feeling". I also thought that if there is something mysterious leading statisticians/bioinformaticians to categorize data, one may use "sliding windows" 0-9 ; 10-19; ..... 1-10 ; 11-20; .... . . 9-18 ; 19-28; ..... and then recheck the results ...
written 6 months ago by english.server210
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Comment: C: Survival analysis: Why to categorize age?
... Thank you. It seems I still have to study more. ...
written 6 months ago by english.server210

Latest awards to english.server

Popular Question 27 days ago, created a question with more than 1,000 views. For Analyze RNA-data directly from SRA database and through Galaxy web tool
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Analyze RNA-data directly from SRA database and through Galaxy web tool
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Analyze RNA-data directly from SRA database and through Galaxy web tool
Popular Question 3 months ago, created a question with more than 1,000 views. For Analyze RNA-data directly from SRA database and through Galaxy web tool
Popular Question 3 months ago, created a question with more than 1,000 views. For Tophat's Mean Inner Distance between Mate Pairs
Popular Question 4 months ago, created a question with more than 1,000 views. For Analyze RNA-data directly from SRA database and through Galaxy web tool
Popular Question 4 months ago, created a question with more than 1,000 views. For Tophat's Mean Inner Distance between Mate Pairs
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Popular Question 6 months ago, created a question with more than 1,000 views. For Analyze RNA-data directly from SRA database and through Galaxy web tool
Student 17 months ago, asked a question with at least 3 up-votes. For Predicting new values from a model.
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Scholar 2.2 years ago, created an answer that has been accepted. For A: Tophat's Mean Inner Distance between Mate Pairs
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Are the values in geo .soft files log2 transformed or normalized?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Tophat's Mean Inner Distance between Mate Pairs
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Analyze RNA-data directly from SRA database and through Galaxy web tool

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