User: zhangyunjie1992

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Posts by zhangyunjie1992

<prev • 12 results • page 1 of 2 • next >
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How to handle data_RNA_Seq_v2_expression_median from TCGA
... hi, I currently downloaded the data_RNA_Seq_v2_expression_median.txt from cbioportal. I found the read_counts is not integer and I don't know how to process this type of normalized data with Deseq2. Should I download the previous-leveled data from portal and use Deseq2 from bottom to the top, or is ...
tcga rna-seq written 14 months ago by zhangyunjie199220 • updated 4 months ago by biostar4155730k
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Comment: C: Problem with LARGE MATRIX
... Hello world! I found out my problem! If you want to screen the Logrank-p value by using the code above, please pay attention to pre processing your expression matrix! The expression matrix should contain no NA and no constant 0 for a gene. And of course it should be perfectly aligned with the clini ...
written 14 months ago by zhangyunjie199220
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Comment: C: Problem with LARGE MATRIX
... Thank you mbuvcm for inspiring me on this one. Your are right, the problem lies somewhere in the matrix. The matrix contained indeed pure numeric content without NA. There are genes showing constant 0 read, so when using survdiff(), there exists no "high" or "low" group. ...
written 14 months ago by zhangyunjie199220
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Comment: C: Problem with LARGE MATRIX
... Hi Santosh Really appreciated it! You are right! The problem is not about the size. It is because in my expression matrix, there are genes showing constant 0 read, so when using survdiff(), there exists no "high" or "low" group. ...
written 14 months ago by zhangyunjie199220
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Comment: C: Problem with LARGE MATRIX
... Hi genomax, Thanks a lot for the reply. Honestly I'm very new to R and always want to achieve what I want by all means. Very helpful suggestion, I will not try to once more use excel to pre process the data downloaded from TCGA and by using R instead. Thanks for the moderation on the code. Really a ...
written 14 months ago by zhangyunjie199220
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Problem with LARGE MATRIX
... Hi everyone, I'm currently handling the TCGA clinical data aligned with gene sequencing data by R. I want to analyze the logrank-p value for every gene in order to find those genes related to OS of the patients. However, when I tried to import the sequencing data into R, and as.matrix() it, it see ...
gene R k-m written 14 months ago by zhangyunjie199220
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How could make this super cool p-value for all genes for specific query by R or any online tool?
... Hey guy, I've recently been using an online analysis tool based on tcga called http://www.oncolnc.org It's so cool! With TCGA expression data and the patient follow-up data, this online tool can actually create a list of gene, with these 'p-values'https://ibb.co/hpOyrQ and stuffs,and all the data w ...
R kaplan meier written 17 months ago by zhangyunjie199220
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Comment: C: No positive results after SAM
... Thanks for the reply russhh, The sample were osteosarcoma biopsies before the surgery and after the preoperative chemotherapy and was graded I to IV according to the viable tumor cell, in another word, the less the viable tumor, the better the response to the therapy. Actually these data were GSE8 ...
written 17 months ago by zhangyunjie199220
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Comment: C: No positive results after SAM
... Appreciate it Devon! I'll try it right away. ...
written 17 months ago by zhangyunjie199220
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Comment: C: No positive results after SAM
... The fact is, other than using SAM, I have processed the data using Excel to calculate the average, foldchange and p-value. For FDR i used q-value(i)=p(i)*length(p)/rank(p), but no FDR was under 0.05. I don't think change the algorithm can make such a big change. But I will try since I can learn to u ...
written 17 months ago by zhangyunjie199220

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