User: Bioinfo

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Bioinfo210
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Posts by Bioinfo

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Comment: C: Expression of specific genes between tumor and normal
... Sure. how to normalize count data in edgeR? And for boxplot can I plot using logCPM? ...
written 2 days ago by Bioinfo210
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Comment: C: Expression of specific genes between tumor and normal
... Hi Nicolas, One general question. If some wet lab scientists asked for the expression of specific genes in tumor and normal samples should I give them counts data of those genes or RPKM, FPKM, CPM, logCPM? ...
written 2 days ago by Bioinfo210
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Comment: C: Heatmap: edgeR counts and DEG
... Take your Differential expressed genes list and get the counts data of those genes. Convert counts to `logCPM` and use that for heatmap. ...
written 2 days ago by Bioinfo210
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Comment: C: Expression of specific genes between tumor and normal
... Thanks a lot for the quick answer. ...
written 2 days ago by Bioinfo210
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Comment: C: Expression of specific genes between tumor and normal
... Is it same when I wanted to check expression of a single gene b/w tumor and normal? Do you recommend t-test if it is a single gene between tumor and normal? ...
written 2 days ago by Bioinfo210
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Expression of specific genes between tumor and normal
... I have RNA-Seq data for 116 tumor and 67 normal samples. Aprrox. 56k genes. Differential analysis can be done b/w tumor and normal with edgeR/ Deseq2. Among those 56k genes, I'm particularly interested in looking at expression of 30 genes between tumor and normals. So, for that do I need to sub ...
differential analysis R rna rna-seq written 2 days ago by Bioinfo210 • updated 2 days ago by Nicolas Rosewick6.5k
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Comment: C: Selecting Deferentially Expressed Genes in RNASeq data analysis - DESEq2 and Cuf
... Yes, In this `res <- results(dds, lfcThreshold = log2(1.5), alpha = 0.1)` is nothing but selecting genes with FC > 1.5 and FDR < 0.1 right? ...
written 4 days ago by Bioinfo210
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Comment: C: Selecting Deferentially Expressed Genes in RNASeq data analysis - DESEq2 and Cuf
... Yes, you are right. So, if I want to select DEGs based on FC > 1.5 and FDR < 0.1 second analysis is the right one. But in this [https://www.biostars.org/p/269582/] e.rempel says that first approach is the right one. ...
written 4 days ago by Bioinfo210
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Comment: C: Selecting Deferentially Expressed Genes in RNASeq data analysis - DESEq2 and Cuf
... Hi Kevin, In Deseq2 to get DEGs based on FDR < 0.1 and FC > 1.5 dds <- DESeq(dds) After this to select siginificant DEGs I have seen two analysis. First analysis: res <- results(dds, alpha = 0.1) res2 <- res[res$log2FoldChange >= 1, ] summary(res2) out of ...
written 4 days ago by Bioinfo210
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Comment: C: Subsampling procedure for differential analysis
... So, I should select common genes from different result sets based on a cutoff? And may I know when I can use subsampling procedure? ...
written 7 days ago by Bioinfo210

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
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Popular Question 4 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
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