User: Andreas Heider

gravatar for Andreas Heider
Reputation:
290
Status:
Trusted
Location:
Last seen:
4 years, 3 months ago
Joined:
8 years, 2 months ago
Email:
a******@trm.uni-leipzig.de

Posts by Andreas Heider

<prev • 34 results • page 1 of 4 • next >
0
votes
4
answers
1.4k
views
4
answers
Comment: C: extract similar expressed genes (SEGs) rather than DEGs
... Dear Aaron, I tried the approach you described and in a short example using the Dilution dataset I came up with a vector of p-values for each feature/gene/transcript. However, I did not understand on which "fit" object to make the calculations. Does it need to be a fit, a lmfit or an eBayes fit-ob ...
written 4.3 years ago by Andreas Heider290
0
votes
4
answers
1.4k
views
4
answers
Answer: A: extract similar expressed genes (SEGs) rather than DEGs
... I am thinking about two one sided test (TOST) or double one sided t-test (DOSTT). Can these be used within LIMMA? I am sure it can be used somewhere, but don't know how. Especially, since one needs the so called "epsilon" to determine the "magnitude of the region of similarity" as written in the do ...
written 4.3 years ago by Andreas Heider290
2
votes
1
answer
844
views
1
answer
tests for equivalence with LIMMA
... Dear BioC community, is it possible with LIMMA to test for equivalence of expression between two sample groups? I am thinking about two one sided test (TOST) or double one sided t-test (DOSTT). I am sure it can be used somewhere, but don't know how. Especially, since one needs the so called "epsi ...
limma differential gene expression equivalence tost dostt written 4.3 years ago by Andreas Heider290 • updated 4.3 years ago by James W. MacDonald50k
0
votes
4
answers
1.4k
views
4
answers
Comment: C: extract similar expressed genes (SEGs) rather than DEGs
... Dear Aaron, thanks for the explanation, however, I think I did not explain the problem in detail. I have a dataset, that has several (10+) phenotypes, in this case celltypes. Exploratory analysis shows, that there are 2 celltypes (let's say A and B), that are similar to each other but different fro ...
written 4.3 years ago by Andreas Heider290
0
votes
4
answers
1.4k
views
4
answers
Answer: A: extract similar expressed genes (SEGs) rather than DEGs
... Hi Steve and Aaron, thanks for your answers!   @Aaron: What you eloborated reads like you are talking about something, that is for exmaple the content of a volcano plot? With the genes consitently expressed in the same manner in let's say the upper right corner? Would it further make sense to p ...
written 4.3 years ago by Andreas Heider290
0
votes
4
answers
1.4k
views
4
answers
Comment: C: extract similar expressed genes (SEGs) rather than DEGs
... Hi Steve and Aaron, thanks for your answers!   @Aaron: What you eloborated reads like you are talking about something, that is for exmaple the content of a volcano plot? With the genes consitently expressed in the same manner in let's say the upper right corner? Would it further make sense to p ...
written 4.3 years ago by Andreas Heider290
5
votes
4
answers
1.4k
views
5 follow
4
answers
extract similar expressed genes (SEGs) rather than DEGs
... Dear BioC community, currently I am searching for a way to extract similar expressed genes in contrast to standard DEGs. Is there a way to achieve this by using already available packages, maybe LIMMA? OH, I am working with single channel data, all aggregated in an ExpressionSet. I have the right ...
microarray limma written 4.3 years ago by Andreas Heider290 • updated 4.3 years ago by Sean Davis21k
0
votes
0
answers
554
views
0
answers
two color arrays, LIMMA and GOstats analysis
... Dear mailing list, I try to get a final solution to the following problem: I have two color microarray data (common reference, dye-swap, multi-factor, multi- group) of which I want to extract differentially expressed genes (DEGs) using LIMMA. Those DEGs I want to analyse for the over-representation ...
clustering graph written 6.2 years ago by Andreas Heider290
0
votes
2
answers
2.0k
views
2
answers
Comment: C: Have troubles with finding Annotations for Bovine and Rhesus\' platforms
... Dear Kaj, I suggest replacing your eArray output file with the former mentioned "015354_D_GeneList_20061130.txt" (from http://www.chem.agilent.com/cag/bsp/gene_lists.asp), because the latter one is much cleaner! Then move R into the directory containing "015354_D_GeneList_20061130.txt" and try the f ...
written 6.2 years ago by Andreas Heider290
0
votes
2
answers
2.0k
views
2
answers
Answer: A: Have troubles with finding Annotations for Bovine and Rhesus\' platforms
... Dear Kaj, Jim was mostly correct. You will have to setup a annotation package for your bovine chip, but don't worry, you can use Affymetrix' annotation files to get it done using AnnotationForge. For your Rhesus chip you could try to use the org.Mmu.eg.db or rhesus.db0 packages, but will need to con ...
written 6.3 years ago by Andreas Heider290

Latest awards to Andreas Heider

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 118 users visited in the last hour