User: Ming Yi

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Ming Yi340
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Posts by Ming Yi

<prev • 34 results • page 1 of 4 • next >
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Answer: A: Questions about multi-factor contrast setting in DESeq2
... Hi, Mike: Thx so much for your very detailed information and advcie on how to set up the contrasts in DESeq2. And the method is brilliant and relatively easy as well. Just to confirm with what I did, I listed some contrasts that I set up based on your way for your to confirm: so for my mode ...
written 4.2 years ago by Ming Yi340
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Comment: C: edgeR design matrix, one group vs average of other groups
... Hi, Yunshun and Georg: I have dataset with a very similar situation. I have a lung cancer dataset with tumors vs normals and amongst them, these tumors have a few subtypes as we believe and hypothesized, I am looking for the difference between the subtypes of tumors, e.g., tumor type 1 vs tumor t ...
written 4.2 years ago by Ming Yi340
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Comment: C: DESeq2 in R_devel: a bug?
... Hi, Mike: Thx a lot for the input and advice, which seems a great idea. Appreciated very much! I also come up a way using combined terms of Type and RasType, which seems rather easy to derive the desired contrasts: > targets<-data.frame(targets,paste(targets$RasType, targets$Type,sep=".")) ...
written 4.2 years ago by Ming Yi340
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Comment: C: DESeq2 in R_devel: a bug?
... Hi, Mike: Thanks for the help. Now we have updated the R and bioconductor version as well as the DESeq2. Here is sessionInfo() R version 3.0.3 (2014-03-06) Platform: x86_64-unknown-linux-gnu (64-bit) [1] DESeq2_1.2.10 All the function calls now seem working, But I still got some issues for t ...
written 4.2 years ago by Ming Yi340
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Comment: C: DESeq2 in R_devel: a bug?
... Hi, Sean: Thx for the reminder. I usually included those info, just too many info for a single email. And turns out to be the key this time. Thx and best Ming Date: Sun, 9 Mar 2014 16:29:01 -0400 Subject: Re: [BioC] Questions about multi-factor contrast setting in DESeq2 From: sdavis2@mail.nih.go ...
written 4.2 years ago by Ming Yi340
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Comment: C: DESeq2 in R_devel: a bug?
... Hi, Mike: Thanks for the info! Yes, your suggestion, since I did check the function, which seems not having the contrast parameter for function results, and the sessioninfo() did show our version in our server may be a bit old. I will get the new version and test again. Thx again and best Ming > ...
written 4.2 years ago by Ming Yi340
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Comment: C: DESeq2 in R_devel: a bug?
... Hi, Mike: Thx for your advice again and I did try what you suggested as below: > dds <- DESeqDataSetFromMatrix(countData = countD,colData = colD,design = ~Type + RasType + Type:RasType); > dds <- DESeq(dds); estimating size factors estimating dispersions gene-wise dispersion estimates ...
written 4.2 years ago by Ming Yi340
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Comment: C: DESeq2 in R_devel: a bug?
... Hi, Mike: Thx for the info and advice. I generally agreed that what you suggested is one of the many ways to explore and then diasect the data for genes that behaved in certain ways. But what I am looking for here is more of non-biased approach looking for a certain refined contrasts and then on to ...
written 4.2 years ago by Ming Yi340
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Comment: C: DESeq2 in R_devel: a bug?
... Hi, Mike: Thx for the info, indeed I did try the following before with the following for the data in user guide: > dds <- DESeqDataSetFromMatrix(countData = countData,colData = colData, design = ~ condition+type) > dds <- DESeq(dds) > resultsNames(dds) [1] "Intercept" ...
written 4.2 years ago by Ming Yi340
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Comment: C: DESeq2 in R_devel: a bug?
... Hi, Mike and All: I am testing DESeq2 for multi-factor contrast setting for my own data with more complex meta data but currently use the simpler dataset from the user guide for testing purpose, and run into some issues that need your input and advice. Here are the commands (only show some more ...
written 4.2 years ago by Ming Yi340

Latest awards to Ming Yi

Popular Question 4.2 years ago, created a question with more than 1,000 views. For limma-voom
Popular Question 4.2 years ago, created a question with more than 1,000 views. For DESeq2 - input data questions

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