User: Andy91

gravatar for Andy91
Andy9160
Reputation:
60
Status:
New User
Location:
Netherlands
Last seen:
10 months, 2 weeks ago
Joined:
3 years, 2 months ago
Email:
a**********@gmail.com

Posts by Andy91

<prev • 17 results • page 1 of 2 • next >
0
votes
1
answers
305
views
1
answers
Comment: C: edgeR trended or tagwise
... I see, thank you for the answer. So even if the NB dispersion is known, you should not use tagwise dispersion for glmQLFit. In which situation would you use tagwise dispersion? Or is it simply a diagnostic measure. ...
written 11 months ago by Andy9160
0
votes
1
answers
305
views
1
answers
Comment: C: edgeR trended or tagwise
... I see, I guess my understanding of the BH method is currently lacking, I'll read more into that. Thank you for the answer ...
written 11 months ago by Andy9160
3
votes
1
answer
305
views
1
answer
edgeR trended or tagwise
... Dear Bioconductor, I am currently performing an RNAseq analysis on rat samples using edgeR. Data was aligned using STAR against the rat genome (Rnor v6.0) and the genes were counted using featureCounts against the Ensembl Rnor gtf file. The experimental design comprises two factors: DSS and stimul ...
edger glmqlftest() written 11 months ago by Andy9160 • updated 11 months ago by Aaron Lun21k
0
votes
2
answers
598
views
2
answers
Comment: C: Error using read.metharray.exp in minfi to read idat files
... Hi Kasper, I think at this point there is not much extra you could do, in the manual the entry for read.meth.exp states that the base argument represents the base directory, at most you could perhaps make a note that this represents the full/relative from the working directory path to the directory ...
written 13 months ago by Andy9160
0
votes
1
answers
285
views
1
answers
Answer: A: Receiving error trying to import matrix into DESeq2
... I cannot say anything about your count matrix as you would have to provide an example of it (i.e. head(countData)). The error seems to suggest that your provided design matrix ("colData") is not well designed. If the provided example is what you are using, the issue would be that the "Age" object c ...
written 13 months ago by Andy9160
0
votes
2
answers
598
views
2
answers
Comment: C: Error using read.metharray.exp in minfi to read idat files
... So I was able to reproduce your error using the minfiData on Bioconductor. The "Basename" column in your samplesheet should contain the full/relative path to the IDAT files, i.e. "/home/poojitha/idats/5684819001_R01C01". The easiest way out IMO is to use the function read.metharray.sheet([base_dire ...
written 13 months ago by Andy9160
0
votes
2
answers
598
views
2
answers
Comment: C: Error using read.metharray.exp in minfi to read idat files
... Could you show the directory structure of the location where all your .idat files are located? Are they located in subfolders, or are they all located in the same folder? How does your samplesheet look like? ...
written 13 months ago by Andy9160
0
votes
1
answers
413
views
1
answers
Comment: C: PCA plot for TPM data
... I would recommend you do some reading on plotting in R. Example tutorials: http://www.cyclismo.org/tutorial/R/plotting.html http://www.cyclismo.org/tutorial/R/intermediatePlotting.html http://tutorials.iq.harvard.edu/R/Rgraphics/Rgraphics.html   Pertaining the question at hand, you could us ...
written 13 months ago by Andy9160
0
votes
1
answers
413
views
1
answers
Answer: A: PCA plot for TPM data
... You can do it with base R. One way of doing it is first transposing the TPM count matrix (assuming you want to run PCA on the samples rather than the genes), centering it, then doing an SVD and subsequently plotting the first and second columns of the u matrix (assuming you are interested in the fir ...
written 13 months ago by Andy9160
0
votes
2
answers
598
views
2
answers
Answer: A: Error using read.metharray.exp in minfi to read idat files
... One oddity I observe in your output is that the zeros of the plate position have been replaced with an "O". This does not appear to be the case for the plate IDs. ...
written 13 months ago by Andy9160

Latest awards to Andy91

Popular Question 21 months ago, created a question with more than 1,000 views. For Understanding contrasts limma

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 191 users visited in the last hour