User: vd4mmind

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vd4mmind0
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Posts by vd4mmind

<prev • 25 results • page 1 of 3 • next >
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Comment: C: Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
... Sure thing, I have already intimated this to my collaborator about the usage of v86 , I will still confirm it once again. Thanks ...
written 4 months ago by vd4mmind0
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Comment: C: Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
... Perfect, works and yes it is ENSEMBLE annotation that I should be using for this project. I did not have that information from my collaborators , that is why I had the discrepancy. Thanks ...
written 4 months ago by vd4mmind0
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Comment: C: Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
... Makes sense. Yes, these are entrezID based. Thanks a lot. Will take a look and try to use the ENSEMBLE library. P.S: removed the edgeR tag.  ...
written 4 months ago by vd4mmind0
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Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
... Hi, I have some issues while using AnnotationDbi to convert my ENSEMBLE IDs to GENE SYMBOLS. I believe the below code should work but there are a lot of NA's I am getting , some of which I understand is fine but some do have gene symbols when I look in ENSEMBLE website for those ENSG ids but I am n ...
annotation annotationdbi ensembl written 4 months ago by vd4mmind0
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Comment: C: edger glmQLFit mix glmLRT
... I do not think, there is a need to retire glmLRT and definitely people using it without reading the manuals or proper understanding and clarification. Well till date I never had the need of glmQLFit , so I was pretty happy with glmFIT + glmLRT. It was need I found in a collaborator so I started digg ...
written 5 months ago by vd4mmind0
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Comment: C: edger glmQLFit mix glmLRT
... Thanks a lot and appreciate the clarification, I also performed the test and found this discrepancy of using QLFIT+LRT gives massive number of DEGs. When I perform QLFit +QLFTest(1 DEG with FDR 0.05) and glmFit+LRT (No degs), obviously my design is not clean since there I have no WT and my ctrl are ...
written 5 months ago by vd4mmind0
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Comment: C: Is there are better way to improve the design via blocking or contrasts while us
... Thanks for your reply. I am not using SVA as covariates in the model. I just did the batch correction with our data and the public data not for using them for DE, but to project the DEGs that I find in public data and to see how they behave in both our data and public data. We also have tumors in ou ...
written 12 months ago by vd4mmind0
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Comment: C: Is there are better way to improve the design via blocking or contrasts while us
... Dear Aaron, I re-did the analysis, and what I did here is first performing SVA on my the public data and our data(I want to project all data together), correct them for the confounders. I need to find actually the difference within the public data as I said between class of T2 vs T1.  However, sinc ...
written 12 months ago by vd4mmind0
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Comment: C: Is there are better way to improve the design via blocking or contrasts while us
... Sure, thanks for the heads up.  ...
written 12 months ago by vd4mmind0
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Comment: C: Is there are better way to improve the design via blocking or contrasts while us
... Thanks for the explanation. I was trying to understand basically why is it wrong to re-estimate the FDR from the limma, as far as I have read, most of these packages are in fact controlling the false discovery rate. Also, we are not guaranteed by the fact that what are the true-positive genes in the ...
written 12 months ago by vd4mmind0

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