User: arfranco

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arfranco130
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Posts by arfranco

<prev • 37 results • page 1 of 4 • next >
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Answer: A: What will lead DESeq2 shows no DEGs if workflow adopted is okay?
... Run a plotPCA like Michael recommends you I had an experiment with 2 conditions and 3 biological replicates. By running a PCA analysis, I noticed that two samples were exchanged (a control was actually a treated sample, and viceversa), and this was enough for not getting a single DE gene ...
written 8 months ago by arfranco130
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What do you do with the DESeq2 NA results ?. How do you manage them ?
... After reading the vignette, I don't actually have a clear idea about what to do with the rows containing NA after a DESeq2 analysis. I am at a loss here. Can you provide with some hints ? ...
deseq2 na values written 22 months ago by arfranco130 • updated 22 months ago by Michael Love26k
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Answer: A: Differential expression of RNA seq data at gene level (for Beginner)
... You can do two similar approaches 1. Map your RNA reads to a reference genome or transcriptome to eventually get a BAM file. This can be accomplished with TopHat, STAR, HISAT ant the like, and need its time and computer power. With this BAM file and with the help of a gtf or gff annotation file, al ...
written 22 months ago by arfranco130
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Answer: A: Generate 3' UTR and 5' UTR ranges from a gff file
... It depends upon it is a model organism or not. If so, try to access to Biomart, where you can generate whatever you want. Another possibility is to convert this gtf file to BED and use Bedtools to get the same answer. To do so, you can access to the bedtools tutorials and help ...
written 23 months ago by arfranco130
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Comment: C: limma. After running a differential expression analysis... Can you get the indiv
... Wondering why in that Elist file, there are two rows for each of the genes.. ¿what is the meaning of that? Daa values are very much similar between the two rows having the same gene name.. What is the origen of that ? Where and how is these data obtained ...
written 2.0 years ago by arfranco130
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Answer: A: limma. After running a differential expression analysis... Can you get the indiv
... I believe that this can be the solution datos_norm1 is the Elist file containing the subtracted, normalized and averaged data processed through the limma functions. I am analyzing a total of 24 arrays ​my_data <- as.data.frame(cbind(datos_norm1$genes, datos_norm1$E)) # Join gene data (names..) ...
written 2.0 years ago by arfranco130
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Answer: A: limma. After running a differential expression analysis... Can you get the indiv
... I'll try to answer myself. Please confirm whether I am right or not.. Let's assume that  data_normalized is a Elist obtained after substracting the background, after a normalizeBetweenArrays normalization, and after running avereps function to average the expression levels.. I believe that the inf ...
written 2.0 years ago by arfranco130
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limma. After running a differential expression analysis... Can you get the individual gene expression levels between individual contrasts for each of the DE genes?
... I am running a DE analysis with limma using a one-color microarray, and got the toptables indicating those genes which are differentially expressed. My colleague (and also myself) want to know, however ,the level of gene expression between individual contrasts for each of the genes that give rise t ...
limma differential gene expression gene expression written 2.0 years ago by arfranco130
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Comment: C: RNA-seq analysis without replicates using tximport and DESeq2
... I am interested in this thread. Would you mind to share your code once done ? ...
written 3.0 years ago by arfranco130
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Answer: A: Very small bug in DESeq2
... I am actually sorry to disturb you. I know the reason and the answer to this problem, and I am not happy at the time of writing these messages I simply wrote this message because my students got very much confused ...
written 3.1 years ago by arfranco130

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