User: Rahil

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Rahil180
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Posts by Rahil

<prev • 111 results • page 1 of 12 • next >
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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 20 days 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 5 weeks 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 8 weeks 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$type) ...
written 9 weeks ago by Rahil180
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Comment: C: Finding a gene signature among multiple group
... Hi @Kevin I'll be very thankful if you advice me on this result. all my 475 genes that I included in this analysis have non-zero coefficient. Call: glmnet(x = data.matrix(modellingLasso[, -1]), y = modellingLasso$type, family = "multinomial", alpha = 0, standardize = TRUE) ...
written 9 weeks 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 9 weeks ago by Rahil180
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Comment: C: Methods for contrasting gene expression profiles between multiple groups
... Thanks @Kevin for your nice explanation. I appreciate if you look at my question [here][1] [1]: https://www.biostars.org/p/462078/ ...
written 9 weeks ago by Rahil180
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Comment: C: Finding a gene signature among multiple group
... As @Kevin said [here][1] I used ANOVA to find genes which are significantly expressed across my four subtypes. To apply ANOVA on all my 580 genes I used this function: AOV <- function(Gene){ y <- df[,c(Gene, "type")] colnames(y)[1]="Gene" anova(aov(Gene~type, ...
written 9 weeks ago by Rahil180
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Finding a gene signature among multiple group
... Hi all, I have a expression profile (RNAseq) of 580 immune-related genes for 350 samples that are already classified into 4 subtypes. I want to find the genes (out 0f 580) that significantly have different expression among these 4 subtypes. In an article Significance analysis of microarrays (SAM) m ...
rnaseq signature sam written 10 weeks ago by Rahil180 • updated 9 weeks ago by Kevin Blighe67k
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Comment: C: how to get ride of duplicated genes when we also have duplicated Ensemble ID in
... Thanks rpolicastro! Oh yes that makes more sense. Is there any package for doing this in r? ...
written 11 weeks ago by Rahil180

Latest awards to Rahil

Centurion 11 weeks ago, created 100 posts.
Appreciated 4 months ago, created a post with more than 5 votes. For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question 4 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 4 months ago, created a question with more than 1,000 views. For Calling CNV using bcftools
Popular Question 4 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 6 months ago, created a question with more than 1,000 views. For Downstream analysis of VCF files obtained from VarScan2
Popular Question 7 months ago, created a question with more than 1,000 views. For Downstream analysis of VCF files obtained from VarScan2
Popular Question 9 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 13 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 21 months ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
Student 2.0 years ago, asked a question with at least 3 up-votes. For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question 2.9 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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