User: Alicia R. Pérez-Porro

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Posts by Alicia R. Pérez-Porro

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Comment: C: DESeq2: up- and down-regulated genes
... Thanks! Just one last thing. I just did results(dds, contrast = c("condition", "NR", "DT")) and the number of most significant genes is the same as before (e.g. NRvsDT = DTvsNR) so I am assuming that the only thing that I am doing by specifying contrast is changing the polarity (what was -log2FC no ...
written 5.4 years ago by Alicia R. Pérez-Porro140
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Comment: C: DESeq2: up- and down-regulated genes
... Hi, I am trying to do: > res <- results( dds, contrast = list( "condition", "NR", "DT" ) ) Error in results(dds, contrast = list("condition", "NR", "DT")) : 'contrast', as a list, should have length 2, see the manual page of ?results for more information And it's giving me an error :( ...
written 5.4 years ago by Alicia R. Pérez-Porro140
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Comment: C: DESeq2: up- and down-regulated genes
... Hi Michael and Simon, Here is my complete script for DESeq2: #open DESeq library("DESeq2") setwd("~/Dropbox/TESIS/DGEA_2.0/Chapter_4_thesis/DE_analysis/DESeq2") #Count matrix input matrix = read.table (file.choose(), header=TRUE, row.names=1) CeleDesign <- data.frame( row.names = colnames( ...
written 5.4 years ago by Alicia R. Pérez-Porro140
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Comment: C: DESeq2: up- and down-regulated genes
... What about this example: (generated with write.table(as.data.frame(resSig[ order( -resSig$log2FoldChange, -resSig$baseMean ),]), file="UpRegulated.txt") transcript_ID baseMean log2FoldChange c99091_g1_i2 433.9095957 4.454648409 c94900_g1_i2 81.89590041 -4.621788185 c95454_g1_i2 85.9 ...
written 5.4 years ago by Alicia R. Pérez-Porro140
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DESeq2: up- and down-regulated genes
... Dear community, I am using DESeq2 to perform my differential expression analyses. My question is, I think, very simple. To interprete the results if I have: > mcols(res, use.names=TRUE) ##To know the level of conditions DataFrame with 6 rows and 2 columns type ...
deseq2 written 5.4 years ago by Alicia R. Pérez-Porro140 • updated 5.4 years ago by Simon Anders3.6k
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Comment: C: DESeq2 transcript level
... Hi Yuan, I emailed the RSEM group to make sure that RSEM isoform counts contain 'multi-isoform' reads. Here is the answer: *"Yes, RSEM explicitly handles reads that map to multiple isoforms in the same way that handles reads that map to multiple genes. eXpress essentially uses the same model as R ...
written 5.5 years ago by Alicia R. Pérez-Porro140
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Comment: C: DESeq2 transcript level
... Hi everyone, Yes, sorry Mike, I forgot to mention that I calculated my isoform counts estimation with RSEM. Thomas, I am aware about the pipeline using RSEM+(edgeR or DESeq) to do DE analysis inside Trinity. I tried and I didn't like just because is not a good option to use with my data. I have no ...
written 5.5 years ago by Alicia R. Pérez-Porro140
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Comment: C: DESeq2 transcript level
... Hi Xiayu, I don't think that I can use Cufflink, I don't have a reference genome, I created my own reference transcriptome. Best, Alicia -- Alicia R. Pérez-Porro PhD candidate Giribet lab Department of Organismic and Evolutionary Biology MCZ labs Harvard University 26 Oxford St, Cambridge MA ...
written 5.5 years ago by Alicia R. Pérez-Porro140
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Comment: C: DESeq2 transcript level
... Hi Mike, Thanks for your answer. I read the explanation from Simon and am still a little bit confuse, reading the edgeR manual I found this: "*edgeR can be applied to di fferential expression at the gene, exon, transcript or tag level. In fact, read counts can be summarized by any genomic feature. ...
written 5.5 years ago by Alicia R. Pérez-Porro140
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DESeq2 transcript level
... Dear Bioconductor users, I am working with differential expression at the transcript (isoform) level. I have 6 different conditions (2 replicates/condition). I want to know if I can use DESeq2 for that or if the package can only be used at the gene level. Thanks, Alicia -- Alicia R. Pérez-Porr ...
deseq2 written 5.5 years ago by Alicia R. Pérez-Porro140 • updated 5.5 years ago by Thomas Girke1.7k

Latest awards to Alicia R. Pérez-Porro

Popular Question 5.4 years ago, created a question with more than 1,000 views. For DESeq2 new error coming up
Popular Question 5.4 years ago, created a question with more than 1,000 views. For DESeq2 transcript level
Popular Question 5.4 years ago, created a question with more than 1,000 views. For DESeq2 new error coming up
Popular Question 5.4 years ago, created a question with more than 1,000 views. For DESeq2: up- and down-regulated genes

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