User: David_emir

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David_emir300
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India
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Posts by David_emir

<prev • 123 results • page 1 of 13 • next >
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Comment: C: MCPcounter Heat map interpretation
... Thanks a lot Kevin, for being such a great help! ...
written 3 months ago by David_emir300
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MCPcounter Heat map interpretation
... Hello all, I am trying to understand the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression data from TCGA and for this, I have used MCPcounter, an R package. Somehow I am not able to understand the Heatmap generated [MCPCounter Heatmap][1]. It wo ...
mcpcounter heatmap written 3 months ago by David_emir300 • updated 3 months ago by Kevin Blighe32k
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Comment: C: MCP counter's problems
... hi maksjytov.nail, I got the same Warning message, did you solve this error? ...
written 3 months ago by David_emir300
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Comment: C: Post Deseq2 Analysis
... HI kevin, Thanks a lot for your kind help. It's of great help to me. I was looking at your code. The input file format is DESeq2 output file or its a count data(I may be stupid in asking this but, sorry for this). I have never used Random forest before, this will be the first time i am gonna use thi ...
written 4 months ago by David_emir300
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Comment: C: Post Deseq2 Analysis
... Hi Kevin, Thanks a lot for your prompt reply, 1. How many genes are statistically significant? I have used the standard filter with padj value of <= 0.05, for genes which show increased expression are (log2 >/= +2) 1438 and the genes which shows decreased expressions are (log2 <= -2) are ...
written 4 months ago by David_emir300 • updated 4 months ago by Kevin Blighe32k
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Comment: C: Post Deseq2 Analysis
... Hi Kevin, Thanks a lot for your help, I am a biologist and I have a limited experience in using coding. I have files on my desk and willing to analyze myself (Cost cutting - funding issue :)). After DGE I have a set of genes which are expressed (+/- log 2 & <=0.05 cut off). I am planning to q ...
written 4 months ago by David_emir300
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Post Deseq2 Analysis
... Hi All, I have Differential gene expression (DGE) results between TCGA-LUSC & TCGA-LUAD samples (LUAD vs. LUSC). I wanted to know what are the ways to take this analysis beyond differential gene expression. How can I use Regression analysis/ Random forest classifications on genes or SVM? Should ...
deseq2 machine learning written 4 months ago by David_emir300
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Comment: C: DESeq2 Error while applying standard analysis
... Thanks, but what the issue? how to get this solved? O God got it! will try with ~status ! i am a such an idiot! ...
written 4 months ago by David_emir300
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Comment: C: DESeq2 Error while applying standard analysis
... Yes, I did notice that but couldn't understand, do you have any idea whats going wrong here? ...
written 4 months ago by David_emir300
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DESeq2 Error while applying standard analysis
... Hi All, I am planning to conduct differential gene expression analysis for lung cancer data set. I have RNAseq count data from two lung cancer subtypes (LUSC & LUAD). I have a matrix of > dim(raw_reads_lusc_luad) # My raw counts data from RNAseq [1] 56830 1035 > head(p ...
deseq2 differential gene expression analysis written 4 months ago by David_emir300

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