User: Merlin

gravatar for Merlin
Merlin 10
Reputation:
10
Status:
New User
Location:
Italy
Last seen:
1 month ago
Joined:
1 year, 1 month ago
Email:
p********@operapadrepio.it

Posts by Merlin

<prev • 31 results • page 1 of 4 • next >
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DESeq2 setting significant p-value
... Hello everyone, I have a question about the p-value that comes out from DESeq2. Here is the command line that I use: res <- results(dds, alpha = 0.05) resultsNames(dds) resLFC <- lfcShrink(dds, coef=2, res=res, type="apeglm") resFile <-na.omit(resLFC) resFile <-res ...
deseq2 written 6 weeks ago by Merlin 10 • updated 5 weeks ago by Michael Love24k
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119
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ReactomePA and genelist
... Hello everyone, I want to use ReactomePA after have performed differential expression analysis. From the bioconductor webite the first codes to run are this library(ReactomePA) data(geneList) de <- names(geneList)[abs(geneList) > 1.5] Is it not clear to me what kind of "geneLis ...
reactomepa written 7 weeks ago by Merlin 10 • updated 5 weeks ago by saicharanp180
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80
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Comment: C: tximport and txOut
... Which one is the paper? probably if I want to do differential gene expression I can just use the default txOut= FALSE while if I want to do analysis at trascript level for the screening of different isoforms I need of txOut= TRUE thanks ...
written 7 weeks ago by Merlin 10
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tximport and txOut
... Hello, I'm using tximport before before running DESeq2. Tximport can summarize counts to gene-level by default or we can avoid gene-level summarization by setting txOut=TRUE using the original transcript level estimation. Can you please tell me what's the correct way for the analysis with DESeq ...
deseq2 tximport written 7 weeks ago by Merlin 10 • updated 7 weeks ago by Michael Love24k
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127
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DESeq and checkFullRank(modelMatrix)
... Hello guys, I am running DESeq2 to compare 4 different conditions and I have a problem with a commmand line. dds = DESeqDataSetFromMatrix(countData = countMatrix, colData = coldata, design = ~ group + treatment +group:treatment) although I found online many others people solved the same prob ...
deseq2 rna written 8 weeks ago by Merlin 10 • updated 8 weeks ago by Michael Love24k
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110
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DESeq2 statistic and design
... Hello everyone, I am using DESeq2 for DEG analysis. I have a set of experiment which consists of 4 duplicates and it's not clear how to create the design object? Here is my condition: condition<- factor(c (group1 =rep ("treatment1",time=2), group2 = rep("treatment2",time=2), group3= rep(" ...
deseq2 rna written 9 weeks ago by Merlin 10 • updated 9 weeks ago by Michael Love24k
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DESeq2 LFCshring=2 or 4
... Hello Everyone, I am using DESeq2 for DEG analysis. I have a total of 8 samples( 1 duplicate for each condition so 4 different conditions) At this point of the analysis: resultsNames(dds) resLFC <- lfcShrink(dds, coef=4, res=res, type="apeglm") I know that this part is used for shinkin ...
deseq2 written 9 weeks ago by Merlin 10 • updated 9 weeks ago by Michael Love24k
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Comment: C: quant.sf files and tximport, transcripts not recognized
... Thank you for you answer Michael, Yes It’s at least three days that I m checking my work, and I have also tried to put the two messages indicated in the output but it didn’t work because I ddin’t use the complete command =TRUE. Slowly I’m learning everything I’m sorry for taking your time, if you ...
written 10 weeks ago by Merlin 10
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Comment: C: quant.sf files and tximport, transcripts not recognized
... I'm not sure if it's read_tsv that is wrong since I don't have tsv file or there is something more required and related to summarizeToGene function it says this as well, None of the transcripts in the quantification files are present in the first column of tx2gene. Check to see that ...
written 10 weeks ago by Merlin 10
3
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109
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quant.sf files and tximport, transcripts not recognized
... Hello Folks, I generated quant.sf file with Salmon tool and the next step is to Import the transcripts abundance dataset with tximport. I generated the file.csv using the same annotation file used in salmon, > head(tx2gene) TXNAME GENEID 1 ENST00000456328 ...
salmon tximport written 11 weeks ago by Merlin 10 • updated 10 weeks ago by Michael Love24k

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