User: john

gravatar for john
john40
Reputation:
40
Status:
New User
Location:
Germany
Last seen:
2 years, 4 months ago
Joined:
2 years, 8 months ago
Email:
s******@students.uni-mainz.de

Posts by john

<prev • 10 results • page 1 of 1 • next >
0
votes
0
answers
538
views
0
answers
Comment: C: RNASeq time-course analysis with maSigPro: T.fit error when assessing multiple g
... Hello Ryan, I am just curious- did you get any support somewhere or are you even using some other tool and gave up on masigpro? Seems like the developers are not around anymore. I have got some trouble using masigpro as well. ...
written 2.4 years ago by john40
0
votes
1
answer
1.2k
views
1
answer
masigpro Error in terms.formula(formula, data = data) : '.' in formula and no 'data' argument
... Hello fellow researchers, using masigpro i encountered an error which I cant seem to fix. Hopefully someone is working with masigpro as well or the developers are still around. As you can see the p.vector function does what it should with "ncounts" beeing the normalized counts and d_1 the design m ...
masigpro written 2.5 years ago by john40 • updated 18 months ago by paolo.uva0
0
votes
3
answers
1.6k
views
3
answers
Comment: C: [DESEQ2] VST with rlog + normalization (size factor estimation) for downstream (
... Wow Michael you are fast- do you ever sleep? Alright it was my assumption as well that the 0 genes are responsible. Nice that we have clarified this! ...
written 2.5 years ago by john40
0
votes
3
answers
1.6k
views
3
answers
Comment: C: [DESEQ2] VST with rlog + normalization (size factor estimation) for downstream (
... Dear Michael, I did as you said and sent an email to your @gmail.com address. I accidentally included the library("reshape2") - you dont need that, just remove or ignore it. The data is not simulated. Here is the session info: > sessionInfo() R version 3.1.1 (2014-07-10) Platform: i686-pc-linu ...
written 2.5 years ago by john40
3
votes
3
answers
1.6k
views
6 follow
3
answers
[DESEQ2] VST with rlog + normalization (size factor estimation) for downstream (clustering) analysis.
... Hello guys. I am using the rlog transformation from DEseq2 (see first figure) and it produces a strange graph. 1th graph are random numbers. 2nd are the raw counts. 3rd are normalized raw counts etc.  Question1): In the 5th graph- Why are the red dots so close to the x axis? It should more or less ...
normalization deseq2 variancestabilizingtransformation written 2.5 years ago by john40 • updated 15 months ago by minie0
0
votes
2
answers
14k
views
2
answers
Comment: C: [DESEQ2] How to access the normalized data of a DESeqDataSet
... AH yes- I found this: counts.DESeqDataSet <- function(object, normalized=FALSE) { ...} Which is the same I guess.   ...
written 2.7 years ago by john40
0
votes
2
answers
14k
views
2
answers
Comment: C: [DESEQ2] How to access the normalized data of a DESeqDataSet
... Steve, Michael, thanks that really helps me out and answeres my question. It takes quite some time to fully understand the DESeq2 package. I have just downloaded the source code of the package. I found almost all functions like plotCounts() (which is in the "R" folder) but I still cannot find the ...
written 2.7 years ago by john40
3
votes
2
answers
14k
views
2
answers
[DESEQ2] How to access the normalized data of a DESeqDataSet
... Hello guys, By  calling DESeq() on a DESeqDataset it estimates the size factors (normalization) automatically. How can I access this data? I must be stored somewhere. I would like to access the normalized counts. >dds <- DESeq() estimating size factors estimating dispersions gene-wise dispe ...
deseq2 written 2.7 years ago by john40 • updated 2.7 years ago by Steve Lianoglou12k
0
votes
2
answers
4.2k
views
2
answers
Answer: A: [DESeq2] time series strain-specific differences over time
... Hello Michael, You said "So this term is a test for if the mut vs WT fold change is different at minute 60 than at minute 0. " Alright. A gene that has a low pvalue in strainmut.minute60 AND 30 AND 120 AND 180 is then to be considered DE in all time points (compared to 0) between WT and MUT. ---- ...
written 2.7 years ago by john40
8
votes
2
answers
4.2k
views
9 follow
2
answers
[DESeq2] time series strain-specific differences over time
... Hello guys, I am doing some RNA-seq analysis using DESeq2 and following the vignette from here, where they use time points 0,15,30,60 ... 180 min. and two groups (strains) http://www.bioconductor.org/help/workflows/rnaseqGene/ In the time series chapter it says: "Genes with small p values from t ...
timecourse deseq2 written 2.7 years ago by john40

Latest awards to john

Great Question 2.4 years ago, created a question with more than 5,000 views. For [DESEQ2] How to access the normalized data of a DESeqDataSet
Popular Question 2.4 years ago, created a question with more than 1,000 views. For [DESeq2] time series strain-specific differences over time
Popular Question 2.4 years ago, created a question with more than 1,000 views. For [DESeq2] time series strain-specific differences over time
Popular Question 2.4 years ago, created a question with more than 1,000 views. For [DESEQ2] How to access the normalized data of a DESeqDataSet

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 165 users visited in the last hour