User: Rao,Xiayu

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Rao,Xiayu530
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2 years, 5 months ago
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Posts by Rao,Xiayu

<prev • 57 results • page 1 of 6 • next >
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Answer: A: DESeq2 DESeqDataSetFromMatrix problem
... Problem solved. It turns out to be the library issue in the linux system. The code should be fine. Thank you all and Merry Christmas! ...
written 2.9 years ago by Rao,Xiayu530
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Comment: C: DESeq2 DESeqDataSetFromMatrix problem
... > dim(countdata) [1] 20587    69 > dim(colData) [1] 69  1 > class(colData) [1] "data.frame" Thank you for your reply! ...
written 2.9 years ago by Rao,Xiayu530
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DESeq2 DESeqDataSetFromMatrix problem
... Dear list,  I encountered a strange problem when using the DESeqDataSetFromMatrix command from DESeq2. I have set up the countData and colData in the required format the same as the sample data described in the tutorial. The column names of the countdata refer to samples, while the row names refer ...
deseq2 written 2.9 years ago by Rao,Xiayu530
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Comment: C: what causes the difference in the topTable results by the two analyses using lim
... Thank you very much! That's clear.  ...
written 3.2 years ago by Rao,Xiayu530
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what causes the difference in the topTable results by the two analyses using limma?
... Hello, I have a design like below, and I would like to compare (1) cont1 vs. treat1, and (2) cont2 vs. treat2. It is interesting to see that the results are different by analyzing the data in the following 2 ways. For example, the topTables of cont1 vs. treat1 are different using the 2 ways. Could ...
limma toptable written 3.2 years ago by Rao,Xiayu530 • updated 3.2 years ago by Aaron Lun17k
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removeBatchEffect and random effect
... Hi, Ryan and other Limma experts I do need confirmation of the use of removeBatchEffect. I have the design and linear model fitting like the following. Chip is my batch effect, and subject is the random effect. design <- model.matrix(~type+chip) corfit <- duplicateCorrelation(y,design,block= ...
limma written 3.2 years ago by Rao,Xiayu530 • updated 3.2 years ago by Gordon Smyth32k
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Answer: A: limma design matrix and contrast specification for time course PCR data with two
... Hi, Linus There is a section called Time course Experiments (9.6) in the Limma user's guide. You can find the design similar to yours there as well as other designs. Thanks, Xiayu -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On B ...
written 3.3 years ago by Rao,Xiayu530
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Comment: C: Any problem with the design matrix or the contrasts? Thanks
... Hi, Ryan Thanks a lot for your comments! It is good to know that testing for a main effect using only the additive model may not be valid in the presence of an interaction effect, which I agree as I recall that from my statistics course. I did what you suggested and tested for the interaction effec ...
written 3.3 years ago by Rao,Xiayu530
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Comment: C: Any problem with the design matrix or the contrasts? Thanks
... Thank you for your kind suggestion, Federico! I tried your suggested design, and found the result is different. There are 10 sig DEGs in the end. > design <- model.matrix(~0+AR+gender+chip,data=targets) > design ARneg ARpos genderM chip 1 0 1 0 1 2 1 0 0 ...
written 3.3 years ago by Rao,Xiayu530
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Comment: C: removeBatchEffect options: design and covariates
... Thanks a lot! I think you are right. I will do that. But what if the Batch itself was treated as a random effect in the model ?? Can I put it in batch=Batch in the removeBatchEffect command? Sorry but I promise this is the last question. Thank you so much! Xiayu ...
written 3.3 years ago by Rao,Xiayu530 • updated 9 weeks ago by Gordon Smyth32k

Latest awards to Rao,Xiayu

Popular Question 2.4 years ago, created a question with more than 1,000 views. For removeBatchEffect and random effect
Popular Question 2.4 years ago, created a question with more than 1,000 views. For removeBatchEffect and random effect
Popular Question 2.4 years ago, created a question with more than 1,000 views. For DESeq2 DESeqDataSetFromMatrix problem
Popular Question 2.4 years ago, created a question with more than 1,000 views. For DESeq2 DESeqDataSetFromMatrix problem

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