User: ijvechetti

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ijvechetti0
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Posts by ijvechetti

<prev • 20 results • page 1 of 2 • next >
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Design for linear model
... Hello all, I'm trying to understand concepts on the linear model and the best way to design my experiment. I have RNAseq data and my design is 2 groups (H and C) and 2 conditions (E and S). To check for the main effects and the interactions what would be the best design: dds..........design= ~ Co ...
statistic written 7 days ago by ijvechetti0
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Comment: C: DESeq2 likelihood ratio test (LRT) design
... Following up on that: -How would be the best design to look at the differences within the exercise but considering the condition? Any suggestions would be much appreciated. ...
written 8 days ago by ijvechetti0
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Answer: A: DESeq2 likelihood ratio test (LRT) design
... Thanks Michael. I just wanted to double-check ...
written 11 days ago by ijvechetti0
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DESeq2 likelihood ratio test (LRT) design
... Hello all, I was wondering if you guys could help me with the design of my experiment. Sample Condition Exercise HC1 Healthy No HC2 Healthy No HC3 Healthy No CPC1 CP No CPC2 CP No CPC3 CP No HE1 Healthy ...
deseq2 written 12 days ago by ijvechetti0
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RMA for multiple samples
... Hello all, I'm wondering if someone could give me some information about the best way to proceed with my analysis. I have 9 groups and 4-time points, and each group has 3 samples. I'm wondering what is the best strategy statistically speaking. Should I do RMA for all CEL files at once? or do it per ...
rma biostatistic written 10 weeks ago by ijvechetti0 • updated 10 weeks ago by James W. MacDonald51k
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Comment: C: DESeq2 for multiple groups
... Thanks Michael. I think following the workflow, as you suggested, helped me to make my design and do my comparisons. But I still have some doubts in what I'm comparing. Could you give me a hand? I did: Design= ~Condition + Time + Condition:Time (full model) vs ~Condition + Time (reduced model). Th ...
written 3 months ago by ijvechetti0
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Comment: C: CDF not found
... Thank you for your help and for your time. That is what I ended up doing, based on some threads I saw. Thank you for the codes. ...
written 3 months ago by ijvechetti0
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CDF not found
... Hello, I'm having a problem with Affymetrix array for Clariom S Rat When i run I get the follow error: library(affy) data <- ReadAffy() eset <- affy::rma(data) Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain ...
microarray affy written 3 months ago by ijvechetti0 • updated 3 months ago by Guido Hooiveld2.5k
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Comment: C: DESeq2 for multiple groups
... Appreciate your time and understand that. I just edited my comment with a third question. Can you tell me about that question? ...
written 3 months ago by ijvechetti0
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Comment: C: DESeq2 for multiple groups
... Thank you so much. All your answer have helped me to understand better all the commands. I still have some doubts and I was wondering if you could point out what could that be: countData= read.table("miRNAcounts_no-pre.ivan.txt", header=T,row.names=1) colData= read.table ("Factors_No-pre.txt", he ...
written 3 months ago by ijvechetti0

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