## User: laianavarromartin

Reputation:
10
Status:
New User
Location:
Spain
Last seen:
1 year, 6 months ago
Joined:
4 years, 1 month ago
Email:
l****************@gmail.com

#### Posts by laianavarromartin

<prev • 30 results • page 1 of 3 • next >
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...   Hi, I'm having some issues running the "hyperGTest" function from GOstats. I get the following error: Error in initialize(value, ...) :    invalid names for slots of class “GOHyperGResult”: pvalues, oddsRatios, expectedCounts, catToGeneId, organism Here the code I use: library( GO.db) librar ...
written 19 months ago by laianavarromartin10
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... Hi Mike, when you say "which test if any level of stage has a difference"... does that refer between all levels of a factor, or between all levels against the level defined as control? ...
written 2.3 years ago by laianavarromartin10
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... Hi again, Sorry, I have another question...when I do the Walt test the adjusted pvalue is adjusted by the multiple comparisons of many genes. In the case exposed above if I have a factor with 4 levels meaning that If I do a walt test I will end up looking at 6 comparisons of levels by pairs. Should ...
written 2.3 years ago by laianavarromartin10
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Comment: A: LRT test multiple comparisons
... Hi Mike, First of all thanks for all your patience and time dedicated to us. I think I have been mistaken these tests all the time. I have an appointment with a local statistician hoping to help me on this...but I had in my mind that doing the Walt test was similar to a t-test, and doing a LRT was ...
written 2.3 years ago by laianavarromartin10
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... Hi, My question refers to the multiple comparison done by LRT test. I though that this test would compare all the levels of a factor between them, but if I'm not mismatching...it is only comparing all the levels with the one I'm considering the "control" group. This is my experimental design: ...
written 2.3 years ago by laianavarromartin10
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... And why do not include Dose as a factor in the design? I also want to find the genes that are altered by dose regardless of the window of exposure. On the other hand, why the walt test is better than the LRT? To make my life easier I always compare the Walt and LRT to a t-test or to an ANOVA. Does ...
written 2.4 years ago by laianavarromartin10
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... I have another experiment a little more complicated.  Have fish exposed to 3 different compounds at equivalent doses. I want to see which genes are specifically regulated by each compound, and which are common to all of them.  Compound Dose Rep.nested 1 Control 1 ...
written 2.4 years ago by laianavarromartin10
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... ok, just to make sure I understand correctly: 1. I should run the DE as  dds <- DESeqDataSet(se, design = ~window + window:rep.nested + window:dose ) dds$dose <- relevel(dds$dose, "Control") dds <- DESeq (dds) 2. Then I can extract the results for each window separately (comparing 2 d ...
written 2.4 years ago by laianavarromartin10
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... Mike, thanks this is clear now. ...
written 2.4 years ago by laianavarromartin10
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... Apart from choosing the best design, I still do not understand how should we do the LRT. So I come back to my original question: Once I define the full model, should i leave out the variable of interest in the reduced model to be looking at the DE genes that are defined by that variable? So in the ...
written 2.4 years ago by laianavarromartin10

#### Latest awards to laianavarromartin

Popular Question 18 months ago, created a question with more than 1,000 views. For Similar to Tukey Post hoc after ANOVA
Popular Question 18 months ago, created a question with more than 1,000 views. For Choosing a threshold for minimum counts in RNAseq

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