User: Elena Grassi

gravatar for Elena Grassi
Elena Grassi10
Reputation:
10
Status:
New User
Location:
Italy, Rozzano, Humanitas University
Twitter:
vodka_liscia
Last seen:
1 day, 21 hours ago
Joined:
4 years ago
Email:
g*******@gmail.com

Post-doc fellow working as a computational biologist in a "Chromatin and Transcription" lab.

In love with transcription factors and log(n) algorithms.

Posts by Elena Grassi

<prev • 11 results • page 1 of 2 • next >
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Comment: C: DESeq2 and betaPrior
... Must have lost it! Thank you very much for your help! ...
written 12 days ago by Elena Grassi10
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Comment: C: DESeq2 and betaPrior
... Yes, I see. Would you consider the split analysis completely wrong or ok-ish given the huge differences between treated and untreated? ...
written 12 days ago by Elena Grassi10
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Comment: C: DESeq2 and betaPrior
... With betaPrior=FALSE: > res_nobeta[rownames(res_nobeta)==16175,] log2 fold change (MLE): comparison Ino80_ut vs ctrl_ut Wald test p-value: comparison Ino80_ut vs ctrl_ut DataFrame with 1 row and 6 columns        baseMean log2FoldChange     lfcSE       stat    pvalue      padj       <numeric&g ...
written 12 days ago by Elena Grassi10
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Comment: C: DESeq2 and betaPrior
... Yes sorry my bad, I copy and pasted from my notes the wrong line. Repeating the steps now (on an Rdata with the dds object): > res <- results(dds, alpha=0.05, contrast=c("comparison", "Ino80_ut", "ctrl_ut"), parallel=TRUE) > head(res) log2 fold change (MAP): comparison Ino80_ut vs ctrl_ut ...
written 13 days ago by Elena Grassi10
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Comment: A: DESeq2 and betaPrior
... merged_pruned is a data.frame with samples identifiers as colnames, entrez as rownames and counts as values. conditions_pruned has columns conditions_sample, rep, comparison and has samples identifiers as rownames. mincounts is 10, mingroup is 3. dds <- DESeqDataSetFromMatrix(countData = merge ...
written 13 days ago by Elena Grassi10
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Comment: C: DESeq2 and betaPrior
... Sorry I realized that I shoud tell you that these data come from the "together" analysis. THe relevant colData: > d[d$comparison == "ctrl_ut",]           condition_sample rep comparison sizeFactor SID100335        SHC002_ut   1    ctrl_ut  0.9642440 SID100352           luc_ut   1    ctrl_ut  1.0 ...
written 13 days ago by Elena Grassi10
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Comment: C: DESeq2 and betaPrior
... One of the strange genes: the results for one of the UT comparisons: entrez baseMean log2FoldChange lfcSE stat pvalue padj padj_multi 16175 1385.52457620314 2.38144205539228 0.46061579583222 5.170126767124 2.3393525067864e-07 0.0002033801512 ...
written 14 days ago by Elena Grassi10
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Comment: C: DESeq2 and betaPrior
... Yup, everything is coming (thanks for the patience in reading :)). ...
written 14 days ago by Elena Grassi10
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DESeq2 and betaPrior
... Hi, I've recently started using DESeq2 with complex experimental designs and I've stumbled across some facts which I cannot wrap my head around. One of the aims of the experiment is to study the transcriptional response following knockdown of several genes, working both on basal conditions and in an ...
deseq2 biostatistics written 15 days ago by Elena Grassi10
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AnnotationData Packages version and pipeline management
... Hi, in my lab we are thinking about restyling our pipeline management system and would like to exploit as much as possible the wealth of annotations available in the AnnotationData Packages. Our system is based on a set of available scripts for common operations and makefiles and aims at being as ...
annotation docker pipeline written 16 months ago by Elena Grassi10

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