User: neverstop

gravatar for neverstop
neverstop0
Reputation:
0
Status:
New User
Last seen:
3 years, 6 months ago
Joined:
4 years, 10 months ago
Email:
n********@hotmail.it

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by neverstop

<prev • 7 results • page 1 of 1 • next >
2
votes
1
answer
1.4k
views
1
answer
How is the mean-variance plot calculated?
... I'm trying to understand how the mean-variance plot is calculated with the meanVarPlot() of EDASeq package. I tried to reproduce it manually with the code below but the result is very different. Given the expression matrix (row=genes, columns=samples), I used the logarithm to transform the counts b ...
edaseq written 3.5 years ago by neverstop0 • updated 3.5 years ago by Wolfgang Huber13k
0
votes
1
answer
503
views
1
answers
Comment: C: Understanding the output of the exprs() function
... Thank you a lot! ...
written 3.5 years ago by neverstop0
0
votes
1
answer
503
views
1
answers
Comment: C: Understanding the output of the exprs() function
... Thank you. May I ask you another question? Do Affymetrix chips have the same number of probes per probeset? Because I tried to divide 409600 by 32 (16 probes of perfect match and 16 probes of mismatch), and I get 12800, while the number of genes is 12625. ...
written 3.5 years ago by neverstop0
0
votes
1
answer
503
views
1
answers
Comment: C: Understanding the output of the exprs() function
... I've edited the main post ...
written 3.5 years ago by neverstop0
4
votes
1
answer
503
views
1
answer
Understanding the output of the exprs() function
... I'm trying to understand what exprs() function does to an AffyBatch Object. I would expect to get a matrix with a row for every gene/probeset and a column for every sample.    > library(affydata) > data(Dilution) > Dilution AffyBatch object size of arrays=640x640 features (35221 kb) cdf ...
affymetrix microarrays written 3.5 years ago by neverstop0 • updated 3.5 years ago by James W. MacDonald51k
0
votes
0
answers
1.3k
views
0
answers
MAplot: Binning grid too coarse for current (small) bandwidth
... I have 49 samples. I need to compare different normalizations applied to Affymetrix data. A way to do that is by using the function MAplot. The problem is that I get some warnings I don't understand: > MAplot(Data, plot.method="smoothScatter",cex=0.5,cex.main=0.5) Attaching package: ‘hgu133plus ...
affymetrixchip affy affymetrix affymetrics written 4.8 years ago by neverstop0
0
votes
1
answer
1.1k
views
1
answer
RNA degradation plot: why curves are so smooth?
... I'm analysing data from Affymetrix microarrays. I don't understand why I get such smooth curves in the RNA degradation plots. This is what I get: I would expect sharp curves like these: Is there something wrong with the script I used? degradation <- AffyRNAdeg(Data) plotAffyRNAdeg(degradation ...
microarray normalization affymetrix written 4.9 years ago by neverstop0 • updated 4.9 years ago by James W. MacDonald51k

Latest awards to neverstop

Popular Question 3.5 years ago, created a question with more than 1,000 views. For MAplot: Binning grid too coarse for current (small) bandwidth
Popular Question 3.5 years ago, created a question with more than 1,000 views. For RNA degradation plot: why curves are so smooth?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How is the mean-variance plot calculated?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 394 users visited in the last hour