User: ijvechetti

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ijvechetti0
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Posts by ijvechetti

<prev • 16 results • page 1 of 2 • next >
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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 5 weeks ago by ijvechetti0 • updated 5 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 8 weeks 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 8 weeks 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 8 weeks ago by ijvechetti0 • updated 8 weeks 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 9 weeks 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 9 weeks ago by ijvechetti0
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Comment: C: DESeq2 for multiple groups
... Michael, sorry to bother you again, but I'm stuck now in how to add the model.matrix in dds and run the LRT. Following the vignette I did: countData= read.table("file.txt", header=T,row.names=1) colData= read.table ("file.txt", header=T) m1<-model.matrix(~ Condition + Time + Condition:Time, col ...
written 10 weeks ago by ijvechetti0
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Comment: C: DESeq2 for multiple groups
... So I have 9 metals (one is the control) and 4-time points (1,3, 6 and 12 months). Some samples I have 3 replicates and some I have 8. In the 12 months, I have on group missing, because the animals died. Is this helpful? ...
written 10 weeks ago by ijvechetti0
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Comment: C: DESeq2 for multiple groups
... Michael, thanks for your prompt answer. After taking a look at the workflows, I saw that my data goes in "Model matrix not full rank" (missing some groups). That way I though in fitting all the groups, including different time, together and do a contrast for all the comparisons I want to make. Is th ...
written 10 weeks ago by ijvechetti0
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DESeq2 for multiple groups
... Hello, I'm having difficulties to set up the best design for my experiment. I have 9 different groups (different metals) and a time-course (1,3,6 and 9 months). One of those metals will be my control, and I'm trying to see what miRNAs are changing among metals in each time-point and also if there i ...
deseq2 written 10 weeks ago by ijvechetti0 • updated 10 weeks ago by Steve Lianoglou12k

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