## User: Alejandro Reyes

Alejandro Reyes1.7k
Reputation:
1,660
Status:
Trusted
Location:
Dana-Farber Cancer Institute, Boston, USA
@areyesq
Scholar ID:
Last seen:
1 month, 1 week ago
Joined:
7 years, 8 months ago
Email:
a*****************@gmail.com

#### Posts by Alejandro Reyes

<prev • 293 results • page 1 of 30 • next >
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... Hi @acciardo, I think your formulae are not well set up. If you want to add **Library.kit** and **IndSample** as blocking factors, your formulae should look like this:  formulaFullModel = ~ sample + exon + IndSample:exon + Library.kit:exon + Group:exon formulaReducedModel = ~ sample + exo ...
written 6 weeks ago by Alejandro Reyes1.7k
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... Hi justinkablan225, If you want to subset the data for those exons that are significant according to DEXSeq, you can subset as you would subset any data frame:  data(pasillaDEXSeqDataSet, package="pasilla") dxr <- DEXSeq( dxd ) dxr[which( dxr\$padj < 0.1 ),]  Alejandro ...
written 4 months ago by Alejandro Reyes1.7k
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Comment: C: DEXSeq dispersion outlier
... About points 1 and 2, since you have many covariates (rin, ageyears, sex, cohort, oligodendrocytes), it will be hard to distinguish how each of these contribute to the individual counts. It is also hard to say that there is nothing. What happens if you remove all those covariates and just test the c ...
written 5 months ago by Alejandro Reyes1.7k
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... You need two matrices, countData and alternativeCountData: Let's say that for a gene you have 5 junctions for a gene and 4 samples, countData would look like this  1 0 2 3 2 0 1 0 0 9 4 2 2 2 3 3 2 0 1 0  alternativeCountData should look like this:  20 30 10 20 20 30 10 20 20 30 10 ...
written 5 months ago by Alejandro Reyes1.7k
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... **Under null model, what is the hypothesis? Is it that exon/counting bin counts does not depend on condition?** Yes, exactly. **What does alternate hypothesis mean here?** That the counts for an exon are dependent on the condition. **I do not understand this part and if possible can you expl ...
written 5 months ago by Alejandro Reyes1.7k
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Answer: C: DEXSeq dispersion outlier
... Hi Fiona, Thanks for your detail report! It is interesting what you are describing. For these points that with extreme values, have you tried plotting the (log) counts per transcript for those genes in each sample? A possible explanation for this is that of the estimation of log2fold changes fro ...
written 5 months ago by Alejandro Reyes1.7k
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... Sure. If you remove these exons from the object, they won't appear on these plots. However, as Mike mentioned, you could filter genes that are lowly expressed. If a gene is not expressed to begin with, it is not worth testing this gene for differential exon usage. Statistically, you won't have pow ...
written 5 months ago by Alejandro Reyes1.7k
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... Sure. If you remove these exons from the object, they won't appear on these plots. However, as Mike mentioned, you could filter genes that are lowly expressed. If a gene is not expressed to begin with, it is not worth testing this gene for differential exon usage. Statistically, you won't have pow ...
written 5 months ago by Alejandro Reyes1.7k
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... Hi gv, Last time I ran an analysis with 6 samples for a human genome, it took around an hour for the whole pipeline. When you say "It is taking forever to finish this step.", how much time are you referring to? Also, please make sure you are using the latest versions of R and Bioconductor (I coul ...
written 5 months ago by Alejandro Reyes1.7k
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... Hi @justinkablan225, Please follow the instructions from this link: http://bioconductor.org/install/ The first sentence says "The current release of Bioconductor is version 3.8; it works with R version 3.5.3.". As James mentioned, old versions of R and Bioconductor are not supported. This means t ...
written 5 months ago by Alejandro Reyes1.7k

#### Latest awards to Alejandro Reyes

Scholar 9 months ago, created an answer that has been accepted. For A: DEXSeq and Independent filtering
Scholar 2.3 years ago, created an answer that has been accepted. For A: DEXSeqHTML and biomart object
Scholar 2.3 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Translating model formula from DESeq to DEXSeq
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: DEXSeq with mutliple experimental conditions - definig contrasts
Scholar 3.6 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 3.7 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 3.9 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 3.9 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 3.9 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: DEXSeq and Independent filtering
Scholar 3.9 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Centurion 4.8 years ago, created 100 posts.

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