User: arfranco

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arfranco120
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Posts by arfranco

<prev • 33 results • page 1 of 4 • next >
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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 24 days ago by arfranco120
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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 24 days ago by arfranco120
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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 24 days ago by arfranco120
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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 ...
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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 12 months ago by arfranco120
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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 14 months ago by arfranco120
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Comment: C: Very small bug in DESeq2
... Well, look at this code > source("https://bioconductor.org/biocLite.R") Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help > biocLite("pasilla") BioC_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21). Installing package(s) ‘ ...
written 14 months ago by arfranco120
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Answer: A: Very small bug in DESeq2
... I installed the pasilla package with a direct install.package('pasilla') command after defining the bioclite repository with the R command setRepositories() I don't have DESeq package installed, and I know this is actually the problem This is a minor problem, though. It simply represented a seri ...
written 14 months ago by arfranco120
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Very small bug in DESeq2
... I am trying to teach my students the using of DESeq2, and they are repeating the instructions contained into the vignette  And they have found a very small bug. This bug does not appear when the "old" DESeq is installed into your system. But since DESeq2 is recommended, I insisted my students to no ...
software error written 14 months ago by arfranco120
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Answer: A: Limma Elist subsetting
... I forgot to mention I tried that solution as well, but it is not working (is not subsetting) subset <- data[data$E >= 2.3,] Error in object[[a]][i, j, drop = FALSE] : (subscript) logical subscript too long ...
written 18 months ago by arfranco120

Latest awards to arfranco

Popular Question 20 months ago, created a question with more than 1,000 views. For limma p-value and adjusted p-value meaning
Scholar 23 months ago, created an answer that has been accepted. For A: matrix transposing in R
Supporter 2.1 years ago, voted at least 25 times.
Scholar 2.4 years ago, created an answer that has been accepted. For A: matrix transposing in R
Scholar 2.4 years ago, created an answer that has been accepted. For A: matrix transposing in R

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