## User: cagenet34

cagenet3420
Reputation:
20
Status:
New User
Location:
Toulouse, France, INRA
Last seen:
10 months, 3 weeks ago
Joined:
2 years, 1 month ago
Email:
c********@gmail.com

#### Posts by cagenet34

<prev • 18 results • page 1 of 2 • next >
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...   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 23 months ago by cagenet3420
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... 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$conditio ... written 23 months ago by cagenet3420 1 answers 523 views 1 answers ... ok thanks for your answer. So basically, from your experience, do you will take them into account for pathway analysis or should I have to discard them ? ... written 23 months ago by cagenet3420 1 answer 523 views 1 answer ... Hi all, Hi, I am using DESeq2 to get differential expression between two genotypes A (sensitive) and B (resistant) and two conditions (virus-infected ; versus control). I’m using the formula given by Mike in DESeq2 vignette "Example 2: two conditions, two genotypes, with an interaction term” which ... written 23 months ago by cagenet3420 • updated 23 months ago by Michael Love18k 2 answers 1.6k views 2 answers ... Hi Anand and Michael, To illustrate that I also have some troubles with few genes that have low read-counts but are DE with a high log2FC threshold. Here is my top DE genes for padj <0.01 and |log2FC| >2. See For example Gene G1 : lo2FC= - 22.01 BUT mean condition 1 (BC.mean)= 59.93 and 0 for ... written 23 months ago by cagenet3420 1 answers 364 views 1 answers ... Hi James, You were right, my problem is that I was not precise as possible. thank for your advice. I didn't know for the useful "apropos" . I do used Google and found some answers BUT as I'm neewbie, I think it was written <NA> and not NA alone. Of course, now everything work fine except that ... written 2.0 years ago by cagenet3420 1 answers 364 views 1 answers ... Yes, I know but my problem is that I don't know how (i'm newbie). So I tried goframeData<- goframeData[-which(row(goframeData)=="<NA>"),] or goframeData<- goframeData[-which(goframeData$EVIDENCE=="<NA>"),] But my goframeData is empty. Finally I proceed in a different way (dow ...
written 2.0 years ago by cagenet3420
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... 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 ...
written 2.0 years ago by cagenet3420 • updated 2.0 years ago by James W. MacDonald46k
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... 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 2.0 years ago by cagenet3420
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... ok Thank you. I'm newbie and your advice helps me ;-)   ...
written 2.0 years ago by cagenet3420

#### Latest awards to cagenet34

Popular Question 23 months ago, created a question with more than 1,000 views. For Error in assay colnames when defining DESeqDataSetFromMatrix following R update

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