User: pablo_garcia05

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Posts by pablo_garcia05

<prev • 10 results • page 1 of 1 • next >
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Answer: A: DESeq2 and edgeR getting very different results
... I recommend to you to take a view of that video (even the whole serie). Here you can see the difference between edgeR and DESeq2 in a simple summary form. StatQuest: edgeR and DESeq2, part 2 - Independent Filtering https://www.youtube.com/watch?v=Gi0JdrxRq5s ...
written 4 weeks ago by pablo_garcia0520
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Comment: C: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
... yes but unfortunately the discussion end at anywhere. However, this kind of discussions are "science" something which is lost nowadays. Researchers are always concerned about go in to open discussion in forums (my experience reading  a lot of them).   ...
written 4 weeks ago by pablo_garcia0520
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Comment: C: contamination and DESeq2 performance
... Thank you MLove for spend your time here. But, in fact what I want to corroborate is the effect of that independent filtering taking our low count genes. Because if that is true, I have a contamination problem in my samples where I found as differentially expressed (few) genes which comes from the g ...
written 4 weeks ago by pablo_garcia0520
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Comment: C: contamination and DESeq2 performance
... I was terrible with my explanation. Yes, part of the design is focused around compare diets. However my problem are those genes assembled from mRNA sequences which come from the digestive tract of my samples. As consequence of the proportion of these material over the RNA extracted from my sample, ...
written 5 weeks ago by pablo_garcia0520
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contamination and DESeq2 performance
... Hello community and in special to M Love, thank you for the support what you give trough this platform, I'm sure you have improved a lot the performance of RNAseq and corrected several fails. I have read about the "problematic" around low count genes and DESeq2, I found several post here in the su ...
deseq2 independent filtering low count genes written 5 weeks ago by pablo_garcia0520 • updated 4 weeks ago by hs.lansdell10
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Comment: C: Effect of lfcThreshold on p-value in DESeq2
... Thank you Ryan. I'm not surprised, I was working with RTqPCR and data analysis is a blackhole even for a technique with more than 15 years-old... RNAseq papers usually has a M&M quite schematic and I have seen a lot of people using software in a wrong way... without any problem to cross "refere ...
written 6 weeks ago by pablo_garcia0520
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Comment: C: Effect of lfcThreshold on p-value in DESeq2
... Very nice explanation, I have just one question. If I have understood you, to apply somekind of LFC filter it must be done by the addition of lfcThreshold option. In this way we conserve the real meaning of the padj result of our FDR test, but if we use: sig_Wild_LA <- Wild_LA[which(Wild_LA$log2 ...
written 6 weeks ago by pablo_garcia0520
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Comment: C: Using 'tximport' library for downstream DGE after quantifying with Kallisto
... Hello Mr Love, thank you for your suggestions to my last questions. I come again with new doubts. I'm doing this DGE with a de novo assembly so I tried to apply your suggestion (in this case I have used EvidentialGene to cluster my transcript to reduce the redundancy). Finally I could manage the co ...
written 8 months ago by pablo_garcia0520
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Comment: C: Using 'tximport' library for downstream DGE after quantifying with Kallisto
... Thank you M. Love and one question, what about to use the output file with the suffix ".genes" produced by Trinity quantification pipeline? for example when I run : $TRINITY_HOME/util/align_and_estimate_abundance.pl --seqType fq \ --left AA_1.fastq \ --right AA_2.fastq \ ...
written 10 months ago by pablo_garcia0520
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Comment: A: Using 'tximport' library for downstream DGE after quantifying with Kallisto
... Hi, I don't wnat to open a new discussion so maybe here I can get help.  When you are working with no identified transcripts from a de novo assembly (Trinity) how do you cover this step? I mean, I don't have a data source for this tx2gene requirement.   Thank you. ...
written 10 months ago by pablo_garcia0520

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