User: Osvaldo

gravatar for Osvaldo
Osvaldo20
Reputation:
20
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New User
Location:
Spain
Last seen:
3 years, 2 months ago
Joined:
5 years, 9 months ago
Email:
o*****@cnio.es

Posts by Osvaldo

<prev • 11 results • page 1 of 2 • next >
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Answer: A: DESEQ2: apparently wrong log2(fold-change) calculation
... opps, I've just seen your last answers.   Thanks, I'll download v1.11.30 ...
written 3.2 years ago by Osvaldo20
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Answer: A: DESEQ2: apparently wrong log2(fold-change) calculation
... yep, sorry.... here you go:   > res log2 fold change (MAP): Intercept Wald test p-value: Intercept DataFrame with 23368 rows and 6 columns               baseMean log2FoldChange      lfcSE       stat        pvalue              <numeric>      <numeric>  <numeric>  <numeric> ...
written 3.2 years ago by Osvaldo20
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Answer: A: DESEQ2: apparently wrong log2(fold-change) calculation
... please find below what is printed out. Thanks!   cds_DESeqED <- DESeq(cds,parallel = TRUE) estimating size factors estimating dispersions gene-wise dispersion estimates: 2 workers mean-dispersion relationship final dispersion estimates, MLE betas: 2 workers fitting model and testing: 2 workers ...
written 3.2 years ago by Osvaldo20
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Answer: A: DESEQ2: apparently wrong log2(fold-change) calculation
... Sure I can show the code. I am pasting it below for this case. Thanks very much !   library("BiocParallel") register(MulticoreParam(2)) library("DESeq2") countTable = read.table("Treatment_3_vs_Ctrl_3.txt",header=TRUE, row.names=1) condition = factor(c("Ctrl_3","Treatment_3")) libType = c("oneFac ...
written 3.2 years ago by Osvaldo20
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DESEQ2: apparently wrong log2(fold-change) calculation
... hi there! My question is related to a DESeq2 output where apparently log2 fold-changes are wrongly calculated.   Let me, please, explain the case with one gene result: Raw counts for that gene (HTSeq-count): Ctrl   2200, Treatment 2097 Normalised counts by DESeq2: Ctrl 2215.349044023 ...
deseq2 differential gene expression log2fc written 3.2 years ago by Osvaldo20
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Answer: A: retrieve human readable gene names from KEGG identifiers
... hi there again ! Although I haven't used the biomaRt package finally, it was a good hint to get to the 'rentrez' R package. I've done it this way: library(rentrez) entrez_summary(db="gene", id="12801")$name [1] "Cnr1" entrez_summary(db="gene", id="13489")$name [1] "Drd2" > entrez_summary(db="ge ...
written 3.4 years ago by Osvaldo20
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Answer: A: retrieve human readable gene names from KEGG identifiers
... Thanks very much for your quick answers !! I will try biomaRt. Robert, I've already tried the function 'translateKEGGID2GeneID', it provides the gene number ID (it simply removes mmu in this case). translateKEGGID2GeneID("mmu:12801") [1] "12801"     ...
written 3.4 years ago by Osvaldo20
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retrieve human readable gene names from KEGG identifiers
... Dear Dr. Zhang, I am starting to use your package KEGGgraph and I've got to a point where I cannot get the information I'd like to get. I've checked the KEGGgraph manual, but I was not able to find a description for that. I am pasting bellow a very small and simple example of what I mean, to try to ...
kegggraph written 3.4 years ago by Osvaldo20
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How to jump from DESeq to DESeq2
... Hi there! I am sending you this question because we've been using DESeq for some of the analysis that we usually perform and now we'd like to jump to DESeq2. We've been checking the DESeq2 manual but it is not clear to us how to switch from one version to the other. Could you please suggest what co ...
deseq deseq2 written 4.1 years ago by Osvaldo20 • updated 4.1 years ago by Michael Love24k
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Comment: C: Unusual results with DESeq ?
... Thanks very much Simon !!! Indeed, you are right, the experiment depth is very low in all the samples, they are going for a new sequencing round with higher depth. I hope results get better then. Anyway, your recommendations will help for future situations like this. best regards. osvaldo On Fri ...
written 5.8 years ago by Osvaldo20

Latest awards to Osvaldo

Popular Question 3.2 years ago, created a question with more than 1,000 views. For DESEQ2: apparently wrong log2(fold-change) calculation
Popular Question 3.2 years ago, created a question with more than 1,000 views. For retrieve human readable gene names from KEGG identifiers

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