User: Picasa

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Picasa320
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Posts by Picasa

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Doubt about batch effect and gene expression analysis
... Hello, I am looking for classical gene expression analysis between 2 conditions with the package `limma`. The problem is that the samples have not been sequenced at the same time so I want to introduce a batch effect. This is my model: design <- model.matrix(~Batch + Condition, data = sam ...
gene expression limma batch written 2 days ago by Picasa320 • updated 2 days ago by Kevin Blighe11k
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Comment: C: Average intron length in Drosophila melagnoster
... Thanks for the code, do you know how to get these statistics but per transcript ? so average intron length per transcript for instance ? ...
written 8 weeks ago by Picasa320
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Intron size from gtf/gff file ?
... Hello, I have an annotation file produced by maker (gff). I am looking for a script that either extract the intron sequence (all combined) per gene or the intron total size per gene. I am kind of stuck with this, so I would be grateful with any help. Thanks ...
annotation intron written 8 weeks ago by Picasa320 • updated 8 weeks ago by Hussain Ather680
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Comment: C: PCA in a RNA seq analysis
... Sorry I forget the txi objet (I have edited it). What is the normalization method in norm <- counts(dds, normalized=TRUE) ? ...
written 9 weeks ago by Picasa320
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Comment: C: PCA in a RNA seq analysis
... Thanks both for your answer. So if I understand: From kallisto results, I can do a PCA and DE analysis using these data: library(edgeR) 1) Import the count: txi <- tximport(files, type = "kallisto", tx2gene = transcript2gene) y <- DGEList(txi$counts) 2) TMM normalisation + lo ...
written 9 weeks ago by Picasa320
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Comment: C: PCA in a RNA seq analysis
... Ok but using the counts is not a problem ? because I have kallisto counts (which are not integers). ...
written 9 weeks ago by Picasa320
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Comment: C: PCA in a RNA seq analysis
... From what I understand, `cpm()` function returns counts per million reads. However, because I have used scaledTPMs instead of real counts, this is equivalent to the initial TPMs used to create the scaledTPMs. But these are additionally normalized by dividing each samples values by the TMM normali ...
written 9 weeks ago by Picasa320
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Comment: C: PCA in a RNA seq analysis
... Hi Kevin, Just a question about the PCA, So I have estimated my count with Kallisto, then I have transformed it to "scaledTPM" values, which are obtained by summing the transcript-level TPMs by gene, and multiplying them with the total library size in millions. (See this for more information So ...
written 9 weeks ago by Picasa320
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Gene expression PCA with DESeq2 filtration
... Hi, I would like to make a simple PCA at gene level of my RNA samples. I am trying to follow this tutorial: http://bioconductor.org/help/workflows/rnaseqGene/#pre-filtering-the-dataset From what I understand, I need to filtered low expressed genes because they give no information: http://bioco ...
filtration pca rna written 10 weeks ago by Picasa320 • updated 10 weeks ago by Kevin Blighe11k
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Comment: C: Augustus scipio error
... can you explain ? I have the issue ...
written 12 weeks ago by Picasa320

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