User: alva.james

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alva.james0
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Posts by alva.james

<prev • 25 results • page 1 of 3 • next >
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Comment: C: Scran functions not found
... Thank you for your reply. Actually I wanted to use the FindMarker function on my RNA-seq Limma Voom result. Inorder to find the marker genes within the chosen set. Is there any channel where the Findmarker deposited like github or elsewhere ? Also I dont whether its a right apporoach to do so, my a ...
written 9 months ago by alva.james0
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Scran functions not found
... Dear All, I am using R version 3.3.1 (R version 3.3.2 (2016-10-31)) , and trying to run the single cell workflow from here https://www.bioconductor.org/help/workflows/simpleSingleCell/#detecting-marker-genes-between-subpopulations  and when I used the functions from Scran library, its says function ...
scran single-cell written 9 months ago by alva.james0 • updated 9 months ago by Aaron Lun19k
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Comment: C: Multi-factorial design for patient-replicates from different time points using d
... Yeah thanks it works :) ...
written 15 months ago by alva.james0
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Comment: C: Multi-factorial design for patient-replicates from different time points using d
... In my design there is also a dot, as  combined_facPhlike . REL in the design matrix ...
written 15 months ago by alva.james0
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Comment: C: Multi-factorial design for patient-replicates from different time points using d
... Sorry, I am getting error here, at makeContrasts : Error: unexpected symbol in " makeContrasts( ( combined_facPhlike ."   ...
written 15 months ago by alva.james0
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Comment: C: Multi-factorial design for patient-replicates from different time points using d
...  I don't know how you initially concluded that time had no effect; --We initially started to find the DE genes (using Deseq2) between ID and REL of all samples. And the DE genes were very heterogeneous in their expression pattern. And it was very difficult to call it as distinguish expression patter ...
written 15 months ago by alva.james0
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Comment: C: Multi-factorial design for patient-replicates from different time points using d
... Does gene expression change between levels of Time? No, we first started with that (to look into the difference between 2-time levels), but we didn't see any changes between time level but the subtype is driving the difference between samples. ...
written 15 months ago by alva.james0
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Comment: C: Multi-factorial design for patient-replicates from different time points using d
... Thanks Aaron for your time, yes Phlike is PH as it is in my design_table, I just corrected that in my primary question, also model$block. So yes I need the DE genes between PH and Non. Their data is my count and the column names of samples don't have "." so I don't understand why combined_fac should ...
written 15 months ago by alva.james0
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Multi-factorial design for patient-replicates from different time points using duplicate correlation LIMMA Voom
... Hello All, I am trying to implement LIMMA room duplicate correlation strategy for my RNA-seq samples using blocking setup. I need to consider following points into account. 1. My samples are biologically paired and dependent also not all patients has its paired sample. for instance, this is how m ...
limma duplicatecorrelation limma voom written 15 months ago by alva.james0
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Comment: C: Multi-factorial design for patient-replicates from different time points (Deseq2
... Micheal,Thanks for the reply, but I think the question wasn't conveyed clear enough,  here is my question again, My question is to find differentially expressed genes between groups, so here in my example cohort I have 82 samples from approximately 40 patients,  and Some patients are paired means, ...
written 15 months ago by alva.james0

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