User: Jose M Garcia Manteiga

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310
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Italy
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Posts by Jose M Garcia Manteiga

<prev • 32 results • page 1 of 4 • next >
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plotSplice plotting only exons passing the filter makes the plot loose gene structure
... Dear all, I have realised that when doing exon usage analysis through limma and diffSplice, after filtering exons with more than, let's say, 1 cpm in a number of samples, all the DGEList, or fit objects contain only exons passing that filter. That is OK for the fitting and the testing analysis and ...
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calcNormFactors TMM vs RLE - plotMA not centered
... Hi Mark and all, I use calcNormFactors with default (TMM) method usually without problems for RNA-Seq before giving the counts to limma-voom. In one experiment, though, I have noticed that the MA plot for my AvsB comparison has given me a cloud of points not centered around 0. I have checked and ...
normalization edger written 3.1 years ago by Jose M Garcia Manteiga310 • updated 3.1 years ago by Gordon Smyth32k
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(Closed) calcNormFactors TMM vs RLE - plotMA not centered
... Hi Mark and all, I use calcNormFactors with default (TMM) method usually without problems for RNA-Seq before giving the counts to limma-voom. In one experiment, though, I have noticed that the MA plot for my AvsB comparison has given me a cloud of points not centered around 0. I have checked and ...
normalization edger written 3.1 years ago by Jose M Garcia Manteiga310
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Comment: C: What are the best packages to compare multiple DE gene lists?
... Dear Stephane, If I understood well what you need, you could use RankProd package that uses rank product non parametric approach to give a p-value to the genes across different studies based on the ranking they achieve by log2FC. It permits to make such "meta-analyses" comparing lists of genes prod ...
written 3.3 years ago by Jose M Garcia Manteiga310
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Comment: C: Annotation files for bacterial genome RNAseq
... Hi Jose, All the options you have already had from the list work fine. My personal favourite one is to use htseq-count and then DESeq2 in R/Bioconductor. It has a specific function that takes the separate gene-counts table per sample and constructs an experiment-object for you with all the data you ...
written 3.5 years ago by Jose M Garcia Manteiga310
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Comment: C: DEXSeq output - count file
... Hi Alejandro, Thanks for your inspection and troubleshooting. The experiment is made upon HUVEC cells, human endothelial cells. CTRLs are all treated with normoxic condition (~20% O2) for 24 hours, but there are two samples from one batch(plating, treating, RNA isolating, library preparing, and sequ ...
written 3.7 years ago by Jose M Garcia Manteiga310
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Comment: C: DEXSeq output - count file
... Hi Alejandro, Yes, there is a batch effect. There are two experiments, exp1 with Controls and Hypoxia samples at 24h and a second at 48h. However the controls were always at 24h. In DESeq2 (and a limma/voom on exons I have to fetch the plot, I'll send it to you later) pca, you clearly see that the c ...
written 3.7 years ago by Jose M Garcia Manteiga310
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Answer: A: DEXSeq output - count file
... Hi Alejandro, I apologize, I did not see the answer in http://permalink.gmane.org/gmane.science.biology.informatics.conductor /53937 I was waiting for a Bioc... sorry about that. Ok, then those exons with very low log2FC and low p.value would belong, if I got it right, to genes with many differenti ...
written 3.7 years ago by Jose M Garcia Manteiga310
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Comment: C: DEXSeq output - count file
... Hi Alejandro, I solved the problem by re-creating the object ecs.24. I had made one DEXSeq analysis up to the end by first creating an ecs object. Then I just split the ecs object, which already had p.value and other info, and re-run the analysis from sizeFactors on onto the new split ecs.24 object. ...
written 3.7 years ago by Jose M Garcia Manteiga310
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Comment: C: DEXSeq output - count file
... Hi Alejandro, I am analyzing with DEXSeq my data. 4 CTRLs and 2 Treated samples. My design is the following: design(ecs.24) sampleName fileName condition experiment H1 H1 Exon_Martelli_Sample_Martelli_H_1.bam HYPOXIA RUN_2 H2 H2 ...
written 3.7 years ago by Jose M Garcia Manteiga310

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