User: vam3002

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vam30020
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Posts by vam3002

<prev • 5 results • page 1 of 1 • next >
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(Closed) Small RNA alignment
... Hi Everyone, I have smallRNA seq data from 7subjects and I am trying to align them using mirdeep2 aligner. The bowtie log file shows the following stats: # reads processed: 194093 # reads with at least one reported alignment: 70610 (36.38%) # reads that failed to align: 112171 (57.79%) # reads ...
rnaseq smallrna alignment bowtie mirdeep2 written 11 months ago by vam30020
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Comment: C: Differentially expressed genes across multiple conditions
... Thanks James. I am thinking of applying regression equation lm(exp.mat~Age) and use the residual values for differential expression analysis. Do you think it is a correct approach to adjust for age? ...
written 11 months ago by vam30020
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Comment: C: Differentially expressed genes across multiple conditions
... Thanks a lot for your input James. I have one last question- I also want to adjust for age variable. Would model.matrix(~treatments+age) work to remove the effect of age from the results?   ...
written 11 months ago by vam30020
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Comment: C: Differentially expressed genes across multiple conditions
... Hi James, Thanks for your response. So you are saying I should use model.matrix(~treatments) and use contrast.fit(A-Z, B-Z, C-Z, D-Z) to compute pairwise comparisons between control and the other four conditions individually and then use decideTests to query differentially expressed genes across al ...
written 11 months ago by vam30020
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Differentially expressed genes across multiple conditions
... Hi everyone, I have RNA- Seq data from 7 samples with 4 different treatments(A,B,C,D) and one control(Z) (7samples X 5conditions). Now I want to use limma- voom to compute differentially expressed genes(up- regulated and down- regulated) across all four conditions. My question is how do I construct ...
differential gene expression limma voom multiple treatments written 11 months ago by vam30020 • updated 11 months ago by James W. MacDonald50k

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