User: Rahil

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Rahil180
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Posts by Rahil

<prev • 115 results • page 1 of 12 • next >
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How RNAseq input file for ssGSAE should be normalized?
... Hi all, I have RNAseq of 12 mouse models (4 condition) that are all normalized together using Deseq2 (median of ratios). I want to do ssGSEA analysis to see the enrichment of one signature for each sample. Should they be normalized for gene length as well? or can I do it with what I have (normaliz ...
ssgsea normalization gene length written 6 days ago by Rahil180
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Why the result of GSEA and ssGSEA is different?
... Hi all, I have microarray data of two conditions. When I did GSEA using fgsea the signature/ geneset was significantly higher in group1 vs group2. However, when I did ssGSEA and used boxplot to show and assess significancy, that signature it is not significantly enriched in group1? Can anyone ...
ssgsea gsea written 8 days ago by Rahil180
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How to do differential CNA analysis?
... Hi all, I got CNA data from TCGA. They provided putative copy-number calls on 616 cases determined using GISTIC 2.0. The values are -2, -1, 0, 1, 2. I have two groups, high-risk & low-risk. I would like to compare the frequency of CNA for each gene, between two groups. How can I find which ge ...
cna gistic differential analysis written 12 days ago by Rahil180
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Comment: C: Copy number differences between groups
... Hi, I have the same question. Could you find a way to determine which genes are more frequently deleted or amplified in group 1 vs group 2? ...
written 18 days ago by Rahil180
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Normalizing multiple conditons all together
... Hello all, I have expression profile of 5 different conditions with 2 different time point, all in one matrix. I am using RMA to normalize them. Can I normalize them all together? or I have to normalize each condition with control group separately? If I normalize them all together don't I lose the ...
rma time series microarray written 3 months ago by Rahil180
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Answer: A: COnverting mouse gene ID to Human gene ID
... Try this https://www.r-bloggers.com/2016/10/converting-mouse-to-human-gene-names-with-biomart-package/ or this https://syngoportal.org/convert.html ...
written 4 months ago by Rahil180
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Comment: C: PCA in a RNA seq analysis
... Dear @Kevin Is it possible to find the genes that best characterizing each group using PCA? I have 630 genes and 300 samples that are annotated in 4 cancer subtypes, using PCA, 4 groups are clear. I want to find genes that best characterize each subtype. Using PC1 loadings I could find the genes th ...
written 5 months ago by Rahil180
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Comment: C: Finding a gene signature among multiple group
... Many thanks @Kevin for being always helpful! Ah, it was a mistake I change it to alpha =1. Yes, I read that and used cv.glmnet. Then I built a new model with 47 genes/predictors that I got with `rownames(co.se$CMS1)[which(co.se$type > 0)]` finalLasso <- glm(as.factor(modellingLasso$type) ...
written 5 months ago by Rahil180
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Comment: C: Finding a gene signature among multiple group
... Hi @Kevin I'll be very thankful if you advice me on this result. all my 475 genes that I included in this analysis have non-zero coefficient. Call: glmnet(x = data.matrix(modellingLasso[, -1]), y = modellingLasso$type, family = "multinomial", alpha = 0, standardize = TRUE) ...
written 5 months ago by Rahil180
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Comment: C: Finding a gene signature among multiple group
... Thanks @Kevin, after applying anova pval < 0.001 I got 497 genes. Then to do multinomial penalised regression I followed your comprehensive reply in this [post][1] and did every step as you said and now after applying this chunk of the script: g1 <- rownames(co.se$S1)[which(co.se$S1 != 0) ...
written 5 months ago by Rahil180

Latest awards to Rahil

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question 3 months ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
Centurion 6 months ago, created 100 posts.
Appreciated 8 months ago, created a post with more than 5 votes. For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question 8 months ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question 8 months ago, created a question with more than 1,000 views. For Calling CNV using bcftools
Popular Question 8 months ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question 10 months ago, created a question with more than 1,000 views. For Downstream analysis of VCF files obtained from VarScan2
Popular Question 10 months ago, created a question with more than 1,000 views. For Downstream analysis of VCF files obtained from VarScan2
Popular Question 12 months ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question 17 months ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
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Popular Question 2.0 years ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
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Popular Question 3.2 years ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?

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