User: Jack
Jack • 0
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Posts by Jack
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... Dears,
It makes no sense for me to have different GO enrichment results just because I changed the the type of Gene IDs. Can someone help me out by explaining the reason behind this problem?
I got different results of GO enrichement analysis with different keyTypes using clusterprofiler.
I used t ...
written 8 months ago by
Jack • 0
• updated
8 months ago by
Guangchuang Yu • 1.1k
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... Yes, you are right. I think it is good to hear your opinion.
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written 19 months ago by
Jack • 0
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... Thank you very much!!
...
written 19 months ago by
Jack • 0
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... Thank you very much for you advice!
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written 19 months ago by
Jack • 0
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... Hi all,
I want to know how to get a gene expression value for a condition with different replicates.
For example, I have condition M and N, each condition with two replicates M1, M2, N1, N2
I want to get one value to represent the gene expression value (FPKM or TPM) of M, can I just use the mean ...
written 19 months ago by
Jack • 0
• updated
19 months ago by
Gordon Smyth ♦ 37k
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Comment:
C: Strange distribution of logFC
... I wanted to simplify the codes, which made it worse, sorry about that... This is the code I rerun with no saved workspaces, without any changes. It creates the exact the same outputs.
...
written 20 months ago by
Jack • 0
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Comment:
C: Strange distribution of logFC
... Yes, I contructed PvsH, sorry about the negligence. This time it is right
...
written 20 months ago by
Jack • 0
0
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Comment:
C: Strange distribution of logFC
... Thank you for your reminding. The codes have been added in the question.
...
written 20 months ago by
Jack • 0
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... Dear all,
I have RNAseq data of two groups. After doing differential gene expression using edgeR and DESeq2(the results are similar). I found the distribution of logFC is a little strange, having two peaks in the distribution.
My guess would be that most genes are equally enriched in both goups, i ...
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... Hi all
I first use the featureCounts in-build annotation (another post) and get the result.
There are 20454 genes in the results list:
a <- read.table(results_txt, head=TRUE)
dim(a)
[1] 20454 18
snapshot of the results
Since in the featureCounts in-built annotation results, there are ...
written 21 months ago by
Jack • 0
• updated
21 months ago by
James W. MacDonald ♦ 50k
Latest awards to Jack
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Why different filtering criteria using CPM to filter the RNA-seq count data in edgeR have so much influence on the number of DE genes?
Supporter
22 months ago,
voted at least 25 times.
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