User: Alejandro Reyes

gravatar for Alejandro Reyes
Alejandro Reyes1.7k
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Location:
Dana-Farber Cancer Institute, Boston, USA
Twitter:
@areyesq
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Last seen:
45 minutes ago
Joined:
7 years, 9 months ago
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Posts by Alejandro Reyes

<prev • 295 results • page 1 of 30 • next >
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Comment: C: featureCount error - cannot identify gene_id
... You can avoid this behavior by setting the flag `-r=no` in the script dexseq_prepare_annotation.py. With this parameter, these tiny regions that overlap with two different genes are ignored and the genes are not smooshed together. ...
written 1 day ago by Alejandro Reyes1.7k
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Comment: C: error in DEXSeq estimateExonFoldChanges
... Thanks for reporting this. Do you have a reproducible example with data that I could use to debug? ...
written 10 days ago by Alejandro Reyes1.7k
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Answer: A: Issue/Error with DEXSeq design formulae in testForDEU function
... 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 3 months ago by Alejandro Reyes1.7k
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Answer: A: Print Differentially Expressed Exons From Dexseq Results
... 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 6 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 7 months ago by Alejandro Reyes1.7k
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Comment: C: null model and DEXSeqDataSet object in DEXSEQ
... 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 7 months ago by Alejandro Reyes1.7k
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Answer: C: null model and DEXSeqDataSet object in DEXSEQ
... **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 7 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 7 months ago by Alejandro Reyes1.7k
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Comment: C: estimateDispersions calculation for > 500,000 exons for 2 conditions taking fore
... 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 7 months ago by Alejandro Reyes1.7k
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Comment: C: estimateDispersions calculation for > 500,000 exons for 2 conditions taking fore
... 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 7 months ago by Alejandro Reyes1.7k

Latest awards to Alejandro Reyes

Scholar 10 months ago, created an answer that has been accepted. For A: DEXSeq and Independent filtering
Scholar 2.5 years ago, created an answer that has been accepted. For A: DEXSeqHTML and biomart object
Scholar 2.5 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Translating model formula from DESeq to DEXSeq
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: DEXSeq with mutliple experimental conditions - definig contrasts
Scholar 3.7 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 3.8 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 4.0 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 4.0 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 4.0 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: DEXSeq and Independent filtering
Scholar 4.0 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Centurion 4.9 years ago, created 100 posts.

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