User: silas008

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silas008100
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Posts by silas008

<prev • 65 results • page 1 of 7 • next >
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Comment: C: How to perform multiple comparisons using edgeR?
... Hey, Charles. I will send I massage to the edgeR support. This is a little bit confuse to me. Thank you very much again!!! ...
written 10 days ago by silas008100
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Comment: C: How to perform multiple comparisons using edgeR?
... Thank you very much. I have used `glmFit() glmLRT()`. I think it is the best choice for my in this case. Let me ask you a simple question. I know the normalization in edegR follows different rules than a simple normalization. But I can not understand something like this: **edgeR output** ...
written 11 days ago by silas008100
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Comment: C: How to perform multiple comparisons using edgeR?
... Excellent. Thank you very much. ...
written 12 days ago by silas008100
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Comment: C: How to perform multiple comparisons using edgeR?
... Hello, AT point. Thank you for helping. What is the difference between using CONTRASTS followed by loop FOR and using different `glmQLFTest()` for each comparison (like group2 vs group1... group3 vs group2... etc)? Thanks again ...
written 12 days ago by silas008100
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Comment: C: How to perform multiple comparisons using edgeR?
... Hello I think I will follow your first recommendation: `glmFit()` `glmLRT()`. edgeR support also suggest this one as a good option, not only for multiple comparisons but also for group2vsgroup1 comparisons. Since we will validate the best targets of the data by qPCR later, I think we can use it for ...
written 12 days ago by silas008100
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Comment: A: How to perform multiple comparisons using edgeR?
... Hello, Charles. Thanks again. ...
written 12 days ago by silas008100
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Comment: C: How to perform multiple comparisons using edgeR?
... Hello, Charles. Thanks for helping. I am sorry for the late response, I was out of my city in a conference. I think the best option in this case is to check if Deseq2 can do want I need. In the case that `glmFit()` and `glmLRT()` will also provide 1 p value. Do you know exactly why to use `exactT ...
written 13 days ago by silas008100
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How to perform multiple comparisons using edgeR?
... Hello, guys. I did not understant one thing. I found some posts regarding this question but I couldn't find an answer for my question. If I have 4 groups, each one with 3 replicates: 1,1,1,2,2,2,3,3,3,4,4,4, and I want to compare all of them against each other, how can I do that? For exemplo: ...
rna-seq edger written 17 days ago by silas008100
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Comment: C: How to use edgeR to compare multiple conditions to reference condtiion
... Hi, Devon. I did not understant one thing. If I have 4 groups: 1,1,1,2,2,2,3,3,3,4,4,4, and I want to compare all of them against each other, how can I do that? For exemplo: x <- read.delim("table.csv",row.names="genes") group <- factor(c(1,1,1,2,2,2)) y <- DGEList(counts= ...
written 17 days ago by silas008100
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What type of GTF file should I use for miRNAseq analysis?
... Helllo, people! I am using edgeR to analise my small RNAseq data. I got a miRNA GTF file from UCSC site and used htseq to count my reads. When I used edgeR for statistics, I realised the normalization is take acording to the GTF anotation, not from the all mapped reads. Of course there are reads th ...
rna-seq edger mirna written 27 days ago by silas008100

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