User: Firas

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Firas0
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Posts by Firas

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Time course analysis in DESeq2: handling common baseline for two experimental co
... It turns out that the rendering system of the Bioconductor support site for the LaTex equations, at least on my system, is messing up the format. What appears to be `group = p *e (condition,day)` is actually `group=paste(condition,day)`. ...
written 4 weeks ago by Firas0
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Comment: C: Time course analysis in DESeq2: handling common baseline for two experimental co
... I am sure that everyone appreciates both the time and the efforts you're putting here. So, thank you for this. I totally understand that you might not have the time to comment on specific questions beyond the level of software support. For me personally, I really think that it is useful to discuss ...
written 4 weeks ago by Firas0
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Comment: C: Time course analysis in DESeq2: handling common baseline for two experimental co
... Many thanks, Michael, once again for your help. I have been enjoying some background reading to avoid asking further questions (without any clue) and here is the complete code which I arrived at. # construct the samples list Replicate <- factor(rep(1:3,times=8)) Day < ...
written 5 weeks ago by Firas0
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Comment: C: Time course analysis in DESeq2: handling common baseline for two experimental co
... Well, that is exactly what I have. Control (time 0) is the baseline measurement for both conditions. I don't have two controls (I just duplicated it as Sham_0 and Injury_0). Then Sham is treated with surgery, and Injury is treated with surgery and injury. Day0 Control ...
written 6 weeks ago by Firas0
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Comment: C: Time course analysis in DESeq2: handling common baseline for two experimental co
... Thanks again for your help. It must be something that I am doing wrong. Because in my case there are no columns with all zeros. So, this is my samples list (note that I replicated the control as Sham_0 and Injury_0) Sample Replicate Condition Day Sham_0_1 1 Sham 0 Sham_0_ ...
written 7 weeks ago by Firas0
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Comment: C: Time course analysis in DESeq2: handling common baseline for two experimental co
... Thank you very much, Michael, for your reply. How do you remove the column for injury at time 0? mm <- model.matrix(~ condition + day + condition:day) # or mm <- model.matrix(~ condition + day + condition:day, coldata) Executing the above code does not result in a column for in ...
written 7 weeks ago by Firas0
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Comment: C: Time course analysis in DESeq2: handling common baseline for two experimental co
... I am working with a similar dataset to the one of the OP. Is there any chance to elaborate more on how to do: > One use of the control group might be as a baseline for effect sizes - so if you set up a group = p ∗ e (condition,day) condition, and relevelled it so control was the baseline, you c ...
written 7 weeks ago by Firas0
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Comment: C: Rhdf5lib install problems
... I am having the same problem. Is there any chance for some help in order to debug this error? Tried compiling on CentOS 6.2 and Gentoo. Log: ```sh CC H5PL.lo CC H5PLint.lo CC H5PLpath.lo In file included from H5PLpath.c:42: H5PLpath.c: In function 'H5PL__create_path_table': ...
written 7 months ago by Firas0
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Comment: C: soGGi package: Error in .validate_names(rownames, ans_rownames, "assay rownames(
... @Nicolas, Thanks for the bug report and the fix. @Thomas, I submitted a pull request containing Nicolas' fix. Best wishes ...
written 8 months ago by Firas0
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Comment: C: Differential analysis of multiple samples with different time points
... Thank you very much, Rory, for your swift reply.  This is exactly what I want. Best wishes, Firas ...
written 14 months ago by Firas0

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