User: IRAIA.MAIALEN

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Posts by IRAIA.MAIALEN

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Different DEG results using Ballgown and edgeR
... Ok, I understand. Thanks for your clear explanation. I didn't know that this two tools do such different things, I thought they both were to find differentially expressed genes between rna-seq samples. Thanks! ...
written 8 weeks ago by IRAIA.MAIALEN0
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How to change stringtie gene_id names with ref_gene_id when performing featureCount
... Hi everybody! I would like to know if there is a way to change stringtie "gene_id" with "ref_gene_id" when performing featureCount to construct the count table for edgeR. The thing is that I have use stringtie to create a merged gtf file, using all the files I want to compare in the DEG analysis. ...
rna-seq stringtie gene_id featurecount re_gene_id written 8 weeks ago by IRAIA.MAIALEN0 • updated 8 weeks ago by Wei Shi3.0k
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Different DEG results using Ballgown and edgeR
... Hi everybody! I have been trying to analyze some RNA-seq samples. On one hand I have used Ballgown, with and without adjustvars option, to see the DEG results, as from the PCA plot I can see a strong batch effect between replicates collected on the same days. Then on the other hand, I tryed to use e ...
rnaseq edger batch effect ballgown adjustvars written 8 weeks ago by IRAIA.MAIALEN0 • updated 8 weeks ago by Gordon Smyth36k
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Comment: C: Aclaration of batch effect adjust in DE analysis
... Thank you!!!!!! very nice explanation!! I show in the protocol that they do which you are explaining to see the significance, but I didn't know for what it was. And I get confused with the final results. So, fit the model with the batch effect design matrix and do the final test with control and tr ...
written 10 weeks ago by IRAIA.MAIALEN0
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Aclaration of batch effect adjust in DE analysis
... Hi everyone! I have a problem understanding the protocol of edgeR, where a batch effect is adjusted in differential expression analysis (4.2.8). I have also a batch effect in my samples and I have constructed the design matrix like this: > design conditionControl conditionM ...
rnaseq edger batch effect written 10 weeks ago by IRAIA.MAIALEN0 • updated 10 weeks ago by James W. MacDonald49k
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Comment: C: MDS Plot help in edgeR
... Hi Gordon, I am the one that have used the incorrect method (cpm without the prior.count function). But I didn't know about the need of defining te prior.count. I only explained a problem using edgeR with my data in biostars page https://www.biostars.org/p/356810 on how to correct the batch effect ...
written 10 weeks ago by IRAIA.MAIALEN0 • updated 10 weeks ago by Gordon Smyth36k

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