User: vd4mmind

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vd4mmind0
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Posts by vd4mmind

<prev • 19 results • page 1 of 2 • next >
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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 5 weeks 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 5 weeks 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 6 weeks 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 6 weeks ago by vd4mmind0
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Comment: C: Is there are better way to improve the design via blocking or contrasts while us
... I understand what you say but if you consider of genes that are still significant with low fold changes coming as better FDR estimates then one can, in fact, re-estimate the FDR based on avg expression and the logFC if the starting expression set is not filtered. I am using such FDR calculation as m ...
written 6 weeks ago by vd4mmind0
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Is there are better way to improve the design via blocking or contrasts while using limma-voom for the mentioned datasets?
... I have 2 RNA-Seq datasets(tumors) coming from different countries. total samples n1=35(having tumors and normals) that is in-house and n2=99 external(only tumors). When I plot the log normalized data via glMDSplot I see 3 distinct clusters( one of in-house and 2 from the external). I used SVA to cor ...
limma voom rna-seq limma-voom written 6 weeks ago by vd4mmind0 • updated 6 weeks ago by Aaron Lun17k
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Answer: A: How to extract the distrances of the column dendrogram from pheatmap and just pl
... I will close this question. it was pretty straightforward and I found out the object plot. Thanks.  ...
written 7 months ago by vd4mmind0
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How to extract the distrances of the column dendrogram from pheatmap and just plot them with the distance scale?
... I have been using the pheatmap() package for a while now and moved out of traditional heatmap.2. However I, recently came across that the pheatmap is actually scaling post column and row dendrogram after the clustering method is specified which is not done by heatmap.2. So if I just want to plot the ...
hclust dendrogram R pheatmap written 7 months ago by vd4mmind0
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Comment: C: Error in running the ChAMP test runs from vignette
... Finally up and running both locally and also HPC. Cannot work it out in local computer , so installed in HPC, will try to establish everything there. Thanks for the replies. Hope I am able to run it to the best of my usage. ...
written 13 months ago by vd4mmind0
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Comment: C: Error in running the ChAMP test runs from vignette
... ah finally working. I just removed all packages and cancelled the session and restarted and reloaded everything from scratch and seems to work now. I do not even know what the problem was. But thanks for your inputs. ...
written 13 months ago by vd4mmind0

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