User: Yi, Ming NIH/NCI [C]

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Posts by Yi, Ming NIH/NCI [C]

<prev • 10 results • page 1 of 1 • next >
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Comment: C: limma-voom
... Thanks a lot for all of your inputs, which are all very helpful! Indeed, I did use the barcode to get the matched normals for the tumors of the same patients. My normals are all code 11, which are supposed to be solid tissues as Steve mentioned. Also the plotMDS plots seem showing a very separation ...
written 5.8 years ago by Yi, Ming NIH/NCI [C]100
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Answer: A: questions on edgeR package
... Dear Dr. Smyth: Thanks so much for your help and advice. Indeed, I did try to use edger on rounded RSEM processed raw counts, result is quite different, here are the comparisons FYI: Not rounded: > y <- estimateGLMCommonDisp(y, design, verbose=TRUE); Disp = 3.99994 , BCV = 2 After rounded t ...
written 5.8 years ago by Yi, Ming NIH/NCI [C]100
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Comment: C: question on the cutoff for limma package
... Hi, Sean: Thanks a lot for your very nice comments and diagnosis on the issues and share with me. Yes, in general I would more rely on the multiple- test based statistics such as FDR or adjusted p-value etc. However, in this particular situation, we do not have a single candidate for further experi ...
written 8.5 years ago by Yi, Ming NIH/NCI [C]100
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question on the cutoff for limma package
... Dear List: Recently, I used limma package to analyze some miRNA array data. One of the differential lists I derived for one of the contrasts in our limma model just used P.Value <0.01 as cutoff combined FC cutoff, we noticed that in this particular contrast, all the differential miRNAs have rat ...
mirna limma written 8.5 years ago by Yi, Ming NIH/NCI [C]100 • updated 8.5 years ago by Sean Davis21k
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Answer: A: how to do paired t-tests for multiple subgroups [was: warnings or potential prob
... Dear Dr. Smyth: Thanks so much for your very nice diagnosis and clarification, which is very helpful! I am completely confident with what you suggested, and will give a try using your new way for setting the linear model, which looks very interesting. Thanks so much again, Best wishes! Ming ---- ...
written 8.6 years ago by Yi, Ming NIH/NCI [C]100
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Answer: A: warnings or potential problems in limma procedure
... Dear Gordon: Thanks so much for your great diagnosis on my issue. Appreciated very much! I noticied that in your limma code in the lmFit function code if (!is.null(ne)) cat("Coefficients not estimable:", paste(ne, collapse = " "), "\n") ....and .... if (NCOL(fit$coef) > 1) ...
written 8.6 years ago by Yi, Ming NIH/NCI [C]100
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Answer: A: warnings or potential problems in limma procedure
... Hi, Dear List: I am still looking for some explanation or diagnosis about the following potential issue that I am not sure what I did is wrong or fine (I apologize if my previous post is not quite clear to the list) I am using limma to do the paired test on the following setting, my tar object lo ...
written 8.6 years ago by Yi, Ming NIH/NCI [C]100
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warnings or potential problems in limma procedure
... Hi, Dear List: I am still looking for some explanation or diagnosis about the following potential issue that I am not sure what I did is wrong or fine (I apologize if my previous post is not quite clear to the list) I am using limma to do the paired test on the following setting, my tar object l ...
limma category written 8.6 years ago by Yi, Ming NIH/NCI [C]100
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Comment: C: average replicate columns in a matrix
... Dear Dr. Gordon: I saw your reply as below to somebody's question in the BioC mailing list. I already get the password to the list, which is why I can see the list's email, but I still have to wait on the list moderator to review my request for approval and my message is being held because of that. ...
written 8.6 years ago by Yi, Ming NIH/NCI [C]100
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paired samples test in limma package
... Hi, List: I have a question regarding paired samples test in limma package. Here is what I got ####W and B are race ####T and N are tumor and normal(paired by same Samples), respectively ####Samples are individual patients: tar$AccNum######## #### > library(limma); > tar<-readTargets(" ...
limma written 8.6 years ago by Yi, Ming NIH/NCI [C]100

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