User: thibault.lorin34

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Posts by thibault.lorin34

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Get release date for version of DESeq2
... Thanks! Just to keep you updated with this: I switched R version from `3.4.2` to `3.3.2` using the RSwitch utility, and ran my script again. I obtain the same result as was obtained last year \o/ (quite reassuring actually). So the DESeq2 version was indeed the cause of the slight discrepancy betwee ...
written 4 weeks ago by thibault.lorin3420
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Comment: C: Get release date for version of DESeq2
... Could you tell me if the following is correct? If I understand correctly, each version of Bioconductor corresponds to an R version. For instance, Bioconductor versions 3.5 and 3.6 correspond to R version 3.4. Hence, this means that if my R version is 3.4.2 and was installed on Sept. 28th 2017, I c ...
written 4 weeks ago by thibault.lorin3420
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Comment: C: Get release date for version of DESeq2
... I would like to get the release date of the version I'm currently using (1.16.1): does it correspond to the "vignette date" (Oct. 17th 2017)? The R version I am using is R version 3.4.2 (2017-09-28) ...
written 4 weeks ago by thibault.lorin3420
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Get release date for version of DESeq2
... Hi, For some reason I cannot reproduce the results I obtained using DESeq2 around one year ago (the main conclusions are the same, with the same top hits, but the results are marginally changed when it comes to DEGs at the "bottom" of the list). I thought (among many other options) that it might be ...
deseq2 R written 4 weeks ago by thibault.lorin3420 • updated 4 weeks ago by Michael Love18k
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Comment: C: Comparing one condition to multiple others using DESeq2 contrasts
... Thank you @Sean Davis! That is most easily accomplished by three separate calls to `results()`. Yes, this is what I could think of, but I want to compare S1 to S2, S1 to S3, S1 to S4, and then S2 to S3, S4 and S5, etc. Running each with a "one-liner" would have been more convenient B-) ...
written 8 months ago by thibault.lorin3420
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Comment: C: Comparing one condition to multiple others using DESeq2 contrasts
... Do you want to test whether S1 is significantly different from each of S2 through S4? Yes, this is what I'd like. I edited the post! ...
written 8 months ago by thibault.lorin3420
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Comparing one condition to multiple others using DESeq2 contrasts
... I have a design with 7 conditions: S1, S2, S3, (...) S7. I want to compare S1 to S2, S3 and S4 and find the genes overexpressed in S1 compared to each of these samples, i. e. the genes overexpressed in S1 compared to S2 and overexpressed in S1 compared to S3 and overexpressed in S1 compared to S4. ...
deseq2 written 8 months ago by thibault.lorin3420 • updated 8 months ago by Sean Davis21k
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Difference between heatmap using Euclidian distance and Poisson distance
... Using DESeq2 I would like to obtain a heatmap of sample-to-sample distances using the rlog-transformed values. However, I'm not sure if I should use the "Euclidian" distance or the "Poisson" distance (both are suggested here). I have obtained both graphs but don't know which one I should "trust". Wh ...
rnaseq deseq2 euclidean sample distance written 9 months ago by thibault.lorin3420 • updated 9 months ago by Michael Love18k
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Comment: C: Kallisto with tximport gives different results with asymmetrical experimental de
... Thanks Michael! Please correct me if I'm wrong. What I should do is import a sampleTable from a file with the file location info. > head(cond) # A tibble: 6 x 6 sample stade ponte jour lane file <chr> <chr> <chr> <int> <int> <chr> 1 S1_1 ...
written 9 months ago by thibault.lorin3420
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Kallisto with tximport gives different results with asymmetrical experimental design
... Hello all, I had to remove samples from my data and I end up with comparing 3 samples (cond1) vs. 2 samples (cond2) — I know that I'm not in an ideal situation. I want to get the most DEGs. I have run kallisto and import the data in R using `tximport`. The problem is that when I compare 2 vs 1 I d ...
deseq2 tximport kallisto written 9 months ago by thibault.lorin3420 • updated 9 months ago by Michael Love18k

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