User: english.server

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Posts by english.server

<prev • 94 results • page 1 of 10 • next >
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Comment: C: Hazard ratio for many genes (gene signature)
... Thank you for your reply. How may I summarize the resulting 100 coefs/HR? May I *"add"* coef of 100 genes and then use exp() (if I do the analysis on z-scores)? Or use glmnet to predict the effect of simultaneous chang of the 100 genes? Eigengene analysis also sounds great. I wondered if it is pl ...
written 8 weeks ago by english.server210
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Comment: C: Hazard ratio for many genes (gene signature)
... Thank you Dr. Blighe. I have actually tested the genes independently on cancer patients. For genes with significant log-rank test result (after FDR) some down-regulated genes show hazard ratios>1 (and some up-regulatd show HR<1), so their de-regulation is supposed to lengthen the lives of pati ...
written 8 weeks ago by english.server210
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Comment: C: Hazard ratio for many genes (gene signature)
... Thank you. My actual problem is when in genomic studies, we obtain _say_ 100 upregulated and 100 down-regulated genes. How can one predict or find an estimate of, the effect of all these genes on survival? ...
written 8 weeks ago by english.server210
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Comment: C: Hazard ratio for many genes (gene signature)
... Dear i.sudbery , Thank you for your response. I am cognizant of the fact you mentioned; however, actually I am not sure about the very terminology I used for the question. ...
written 8 weeks ago by english.server210
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Hazard ratio for many genes (gene signature)
... I noticed that the Gepia2 web server also accepts more than a single gene as input to calculate log-rank and hazard ratio for TCGA data as if there was only a single gene. A "High" and a "Low" group are internally assigned to the samples by the server. I wondered if the following code/approach is th ...
R survival analysis written 8 weeks ago by english.server210
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Comment: C: Inconsistent survival times in TCGA clinicalMatrix file?
... Firstly, I wish to thank you *indeed* very much for the effort you put into answeing this question. I downloaded the data from Xena browser https://tcga.xenahubs.net/download/TCGA.GBM.sampleMap/GBM_clinicalMatrix The problem was due to the wrong column: CDE_survival_time I chose, instead o ...
written 11 weeks ago by english.server210
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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 11 weeks ago by english.server210 • updated 11 weeks ago by Kevin Blighe66k
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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 11 weeks ago by english.server210
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Comment: C: Too many RNAseq samples. What to do?
... Thanks. I updated the post. ...
written 11 weeks 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 12 weeks ago by english.server210

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