User: IRAIA.MAIALEN

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Posts by IRAIA.MAIALEN

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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 3 months 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 3 months ago by IRAIA.MAIALEN0 • updated 3 months ago by Wei Shi3.1k
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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 4 months ago by IRAIA.MAIALEN0 • updated 3 months ago by Gordon Smyth37k
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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 4 months 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 4 months ago by IRAIA.MAIALEN0 • updated 4 months ago by James W. MacDonald50k
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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 4 months ago by IRAIA.MAIALEN0 • updated 4 months ago by Gordon Smyth37k

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