User: angajalaanusha

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Posts by angajalaanusha

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Chromosomal location mapping for miRNAs
... I have chromosomal location or genome coordinates for list of miRNAs. Please advice me how can I make a figure to better visualize this data ? I am interested in figures like this ( Figure 3) https://www.researchgate.net/figure/Genomic-organization-of-14q32-microRNA-miRNA-clusters-neighboring-the-D ...
cancer written 7 weeks ago by angajalaanusha10 • updated 7 weeks ago by James W. MacDonald50k
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Is it required to specify Outliers function in DESeq2
... Please see following code.I am wondering DESeq() automatically removes the outliers or should I include or specify the outliers function? When I did the analysis in around 100 samples the results looks fine. But in case of higher numbers of samples, the results looks different. Please advice how can ...
deseq2 written 5 months ago by angajalaanusha10 • updated 5 months ago by Michael Love24k
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basemean cut off in DESEQ2
... After the DESEQ2 analysis, the baseMean values from the results range from (0.2 to 87622.00). For the selected results I have used 0.05 FDR cutt off. But, still some baseMeans are as low as 0.2. Can I use the baseMean cut off as 5. My concern is if the baseMean is this low , then the log2FC will ...
deseq2 written 5 months ago by angajalaanusha10
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Comment: C: RESULTS() using contrast=c("condition","A","B"), the results would be A vs B cor
... Thanks a million for answering the question. This link is very helpful. mcols(res, use.names = TRUE) is helpful to know. ...
written 5 months ago by angajalaanusha10
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RESULTS() using contrast=c("condition","A","B"), the results would be A vs B correct?
... I am trying to get know if a gene is down in Condition A vs B.While using results function, I am trying to know if I am doing this correctly. Because, I am not able to see how it is done internally. So my questions are as follows. In my case ( Condition = TNBC status, A = QNBC, B= TNBC ARP. 1. What ...
deseq2 written 5 months ago by angajalaanusha10 • updated 5 months ago by Michael Love24k

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