User: NMostajo

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NMostajo10
Reputation:
10
Status:
New User
Location:
Germany
Last seen:
2 years, 9 months ago
Joined:
2 years, 10 months ago
Email:
n************@gmail.com

Posts by NMostajo

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Comment: C: ResrtingTools include pvalue NA
... I "feel" a bit stupid, I thought the NuLL was working as False, because I was not giving a DataSet. My R experience is recent. Thank you! ...
written 2.8 years ago by NMostajo10
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Comment: C: ResrtingTools include pvalue NA
... publish works when I use the DeseqDataSet (dds) as I wrote in the question, but it does not work with results (thats why I am wondering how to desactivate this pvalue filter) Also, I have tried already: RNA <- results(dds,contrast = c("condition","NA","R"), cooksCutoff = FALSE, independentFilt ...
written 2.8 years ago by NMostajo10
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ResrtingTools include pvalue NA
... Hi! I already asked this, but was combined with another question, therefore I missed the answer I was looking. I have my DeseqDataSet which I want to put in Reporting tools -> dds out <- "/mnt/out/" des2ReportAll <- HTMLReport(shortName = 'RNAseq_analysis_with_DESeq2', title = 'sRNA-seq ...
reportingtools deseq2 na pvalue written 2.8 years ago by NMostajo10 • updated 2.8 years ago by Michael Love23k
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Comment: C: ReportingTools include pvalue NA and comparissons
... You are right was a problem with the versions. thanks! ...
written 2.8 years ago by NMostajo10
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Comment: C: ReportingTools include pvalue NA and comparissons
... I tried from the beginning and I got the same result: dds <- DESeqDataSetFromMatrix(countData = THP1_countData,                               colData = colData_try,                               design = ~ condition) featureData <- data.frame(gene=rownames(THP1_countData)) dds <- dds[ ro ...
written 2.9 years ago by NMostajo10
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Comment: C: How to find genes causing the high variance of one replicate in the PCA
... Thanks! I got my gene IDs ...
written 2.9 years ago by NMostajo10
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Comment: C: ReportingTools include pvalue NA and comparissons
... Sorry, I have run already ReportingTools, and what I get (and I would like to add) Gene names - plots - FC (FC for all comparissons**) : Including the genes with a padj of NA **I understand that the FC of each pairwise comparisons has to be added later My problem is with the padj NA. According to ...
written 2.9 years ago by NMostajo10
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How to find genes causing the high variance of one replicate in the PCA
... Hello,  I have checked the PCA from my sRNAseq data and there is one replicate which goes over 67% away from all my samples (1/18). I know that the PCA plots the genes with the top variance, and this sample seems to not have crazy values in all the genes (checked random), and with PCA of different ...
deseq2 pca variance gene_id written 2.9 years ago by NMostajo10 • updated 2.9 years ago by Michael Love23k
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Comment: C: ReportingTools include pvalue NA and comparissons
... That means that I should run results for the overall dds (until now I only did contrast analysis)? So I do not loose this NA values and run the ReportingTools over this OverallComparisson. If I understood correctly? Then I would have to?? OverallComparisson <- results(dds, cooksCutoff = FALSE) ...
written 2.9 years ago by NMostajo10
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ReportingTools include pvalue NA and comparissons
... Dear all,  I am trying to analyze my smallRNAseq data with Deseq2 and to run ReportingTools on it. I have different treatments and timepoints, I saw that you have a coef option to tell where to do the comparison with, but my data set then will exclude another timepoint or treatment. I am wondering ...
reportingtools deseq2 R pvalue coef written 2.9 years ago by NMostajo10 • updated 2.9 years ago by Michael Love23k

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