User: Biologist

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Biologist150
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Posts by Biologist

<prev • 165 results • page 1 of 17 • next >
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Comment: C: Why median is NA for some of the group outcomes in survival analysis?
... Thanq. I did the plot and I could see median for low group, but no median for high group. The plot looks like this ![survival plot][1] I actually want to know which group is worse or good for prognosis without plotting. If there is a group (high or low) with median `NA` does it mean that group is go ...
written 9 weeks ago by Biologist150
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Why median is NA for some of the group outcomes in survival analysis?
... I have dataframe `data` with columns like FollowUpDays, patient_vital_status and high, low information of a gene. I'm trying to do survival analysis using the Followup information, patient_vital_status and the information of gene. I'm using like below: surv_diff <- survdiff(Surv(FollowUpDay ...
R kaplan-meier survival clinical rna-seq written 9 weeks ago by Biologist150 • updated 9 weeks ago by Jean-Karim Heriche19k
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Comment: C: Error in differential analysis for samples with different time points
... Could you please tell me whether the above way it is right or I should add more samples per treatment? ...
written 3 months ago by Biologist150
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Comment: C: Error in differential analysis for samples with different time points
... But If my coldata looks like below, I don't see any error: coldata: Samples Type Time SampleA Control Day1 SampleB Control Day2 SampleC Control Day3 SampleD Gene_OE Day1 SampleE Gene_OE Day2 SampleF Gene_OE Day3 design2 <- model.matrix(~ 0 + group + coldata$T ...
written 3 months ago by Biologist150
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Error in differential analysis for samples with different time points
... I have 4 samples. 2 control and 2 gene_oe (over expression) samples. I wanted to do differential analysis between Gene_OE vs Control samples. I have the samples column data like following: coldata: Samples Type Time SampleA Control Day1 SampleB Control Day2 SampleD Gene_OE Da ...
differential analysis R rna-seq edger written 3 months ago by Biologist150 • updated 3 months ago by h.mon25k
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Comment: C: genie3 for lncRNAs and mRNAs co-expression
... Instead of using only DE lncRNAs and DE mRNAs, you should input all the mRNAs and lncRNAs with some filtering like removing genes with low expression. You can check the `WGCNA` R package for Co-expression network analysis. ...
written 4 months ago by Biologist150
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Comment: C: Estimating gene set enrichment using Fishers exact test
... Sure thanq. I will have a look. ...
written 4 months ago by Biologist150
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Comment: C: Estimating gene set enrichment using Fishers exact test
... Thanks a ton @Jean-Karim Heriche Here 1000 genes expressed meaning, differentially expressed in tumor or just expressed? And 80 target genes of lncRNA X mean co-expressed genes or neighbouring genes? If it is co-expressed genes what should be the cutoff for selecting target genes? ...
written 4 months ago by Biologist150
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Comment: C: Estimating gene set enrichment using Fishers exact test
... Here in the paper they say "each test was adjusted for the total number of lncRNAs, lncRNA targets, and gene set tested". I'm a bit confused how the contingency table should look for the fishers test in this type of analysis? If you don't mind Could you please tell with a small example mentioning ...
written 4 months ago by Biologist150
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Estimating gene set enrichment using Fishers exact test
... Hi, I'm working with lung cancer data and I'm interested in lncRNAs, I would like to identify lncRNAs that target key pathways. Recently, I read a paper which discusses about this type of analysis. Here is the paper [Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes ...
fisherstest rna-seq gsea lncrna written 4 months ago by Biologist150

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Popular Question 16 days ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
Popular Question 3 months ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
Popular Question 3 months ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
Popular Question 4 months ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
Popular Question 4 months ago, created a question with more than 1,000 views. For Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
Student 6 months ago, asked a question with at least 3 up-votes. For Gene set enrichment analysis with edgeR output
Popular Question 6 months ago, created a question with more than 1,000 views. For How to make a color plot out of three columns from a dataframe in R?
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