User: cagenet34

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cagenet3410
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Toulouse, France, INRA
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2 months, 2 weeks ago
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1 year, 5 months ago
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Posts by cagenet34

<prev • 18 results • page 1 of 2 • next >
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Comment: C: DESeq2 : DE genes witth high log2FC and few or null counts in some samples
...   I also done PCA with DESEQ2 and found nearly 92% for PC1 which is very strange for me...my first axis correspond to genotype and the second one to condition. In fact, I've done all the exploraty analysis and think it was ok but maybe it's not ...       ...
written 15 months ago by cagenet3410
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Comment: C: DESeq2 : DE genes witth high log2FC and few or null counts in some samples
... Yes I did. Here the results for me it's fine ....:  I use ade4 package dds2<-as.data.frame((counts(dds1,norm=FALSE))) lmat<-log(1+dds2) library(ade4) lmatc<-bicenter.wt(lmat) lmatc.pca<-dudi.pca(lmatc,center=F,scale=F,nf=3,scannf=F) s.class(lmatc.pca$co,fac=dds1$genotype:dds1$conditio ...
written 15 months ago by cagenet3410
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Comment: C: DESeq2 : DE genes witth high log2FC and few or null counts in some samples
... ok thanks for your answer. So basically, from your experience, do you will take them into account for pathway analysis  or should I have to discard them ?  ...
written 15 months ago by cagenet3410
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DESeq2 : DE genes witth high log2FC and few or null counts in some samples
... Hi all, Hi, I am using DESeq2 to get differential expression between two genotypes A (sensitive) and B (resistant) and two conditions (virus-infected ; versus control). I’m using the formula given by Mike in DESeq2 vignette "Example 2: two conditions, two genotypes, with an interaction term” which ...
deseq2 written 15 months ago by cagenet3410 • updated 15 months ago by Michael Love14k
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Comment: C: too many genes with low read-counts as differential expressed in DESeq2
... Hi Anand and Michael, To illustrate that I also have some troubles with few genes that have low read-counts but are DE with a high log2FC threshold. Here is my top DE genes for padj <0.01 and |log2FC| >2. See For example Gene G1 : lo2FC= - 22.01 BUT mean condition 1 (BC.mean)= 59.93 and 0 for ...
written 15 months ago by cagenet3410
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Comment: C: Error in GOFrame due to NA for unsupported organism (Gene Ontology)
... Hi James, You were right, my problem is that I was not precise as possible. thank for your advice. I didn't know for the useful "apropos" . I do used Google and found some answers BUT as I'm neewbie, I think it was written <NA> and not NA alone. Of course, now everything work fine except that ...
written 16 months ago by cagenet3410
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Comment: C: Error in GOFrame due to NA for unsupported organism (Gene Ontology)
... Yes, I know but my problem is that I don't know how (i'm newbie). So I tried goframeData<- goframeData[-which(row(goframeData)=="<NA>"),] or goframeData<- goframeData[-which(goframeData$EVIDENCE=="<NA>"),] But my goframeData is empty. Finally I proceed in a different way (dow ...
written 16 months ago by cagenet3410
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Error in GOFrame due to NA for unsupported organism (Gene Ontology)
... Hi all, I'm using reportingTools following RNAseq differential analysis and am having trouble with adding annotation for GO using unsupported model organism (ie sheep, org.Oa.eg.db). Ovis aries (sheep) is not supported by "AnnotationForge" package, so I'm following the instructions from "How To Us ...
gostats reportingtools annotationhub written 16 months ago by cagenet3410 • updated 16 months ago by James W. MacDonald45k
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Answer: A: Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.
... Hi Rinaldo, I also had the same error and your tip works. I change my DGElist object name from "y" to "resDGE" and now it's ok. Thank you for your solution. Carine ...
written 16 months ago by cagenet3410
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Comment: C: Generating database with non model species to be use by ReportingTools
... ok Thank you. I'm newbie and your advice helps me ;-)   ...
written 16 months ago by cagenet3410

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