User: english.server

Reputation:
20
Status:
New User
Location:
Last seen:
3 days, 14 hours ago
Joined:
1 year, 7 months ago
Email:
e*************@gmail.com

Posts by english.server

<prev • 10 results • page 1 of 1 • next >
0
votes
1
answer
128
views
1
answers
Comment: C: How to check whether experimental covariates are confounded with our group of in
... Thank you for your response. I think I've to study a little more to digest the concept. ...
written 21 days ago by english.server20
0
votes
1
answer
128
views
1
answers
Comment: C: How to check whether experimental covariates are confounded with our group of in
... Thank you Gordon Smyth. Regarding my previous post, I *thought* the concepts asked there are different from what is asked here! Thanks for clarification. You are absolutely right about me wanting to "analyse microarray datasets automatically without having to look at plots or think about the variabl ...
written 24 days ago by english.server20
1
vote
1
answer
128
views
1
answer
How to check whether experimental covariates are confounded with our group of interest?
... Hi In the context of microarray analysis, how to check whether experimental covariates (age/gender) are confounded with our grouping of interest (ie diseased vs normal)? goi = sample(letters[1:2], 20, T) # group of interest cov=list() #3 covariates cov$c1=sample(letters[1:4], 20 ...
microarray covariates written 25 days ago by english.server20
0
votes
1
answer
179
views
1
answers
Comment: C: Limma DEG analysis experiment with partial paired design + batch effect
... Great response, and thank you again for your detailed response. I think I got the main ideas. ...
written 5 weeks ago by english.server20
0
votes
1
answer
179
views
1
answers
Comment: C: Limma DEG analysis experiment with partial paired design + batch effect
... Thank you @Gordon Smyth for your analytic response. In geneal, how should one *check* whether factors are confounded? On googling I ended up with chisq.test(). However, chisq.test(a$batch, a$donor) #p-value = 0.2867 chisq.test(a$pair , a$donor) #p-value = 0.01 chisq.test(a$co ...
written 5 weeks ago by english.server20
0
votes
1
answer
179
views
1
answers
Comment: C: Limma DEG analysis experiment with partial paired design + batch effect
... Thank you. I updated the original question according to your post. PS. I also edited the title. ...
written 5 weeks ago by english.server20
6
votes
1
answer
179
views
8 follow
1
answer
Limma DEG analysis experiment with partial paired design + batch effect
... Hi! While re-analyzing GSE65106 from GEO, I have constructed a table containing a subset of samples, as follows: > a # see below for dput(a) accession cond donor batch pair A1.r1 GSM1587362 ASD AA1 1a 1 A1.r2 GSM1587363 ASD AA1 2a 1 A2.r1 ...
limma paired batch written 5 weeks ago by english.server20 • updated 5 weeks ago by Gordon Smyth39k
0
votes
1
answer
386
views
1
answers
Comment: C: affymetrix miRNA microarray analysis, (package mirna30cdf)
... Thank you indeed very much. ...
written 18 months ago by english.server20
1
vote
1
answer
386
views
1
answer
affymetrix miRNA microarray analysis, (package mirna30cdf)
... Hi every one! miRNA 3.0 CDF Library File  is present at affymetrix site However, while I want to use affy (not oligo) for analysis of this type of array, I get the error that mirna30cdf not available. Any help would be appreciated. ...
microarray affy written 18 months ago by english.server20 • updated 18 months ago by James W. MacDonald51k
0
votes
0
answers
316
views
0
answers
Reading in .gpr files
... Hi everyone!   I need to read in .gpr files downloaded from GEO. I cant get either read.maimages {limma} or read.GenePix {marray} working. Where am I wrong? Thank you inn advance. files= dir() files= files [grep(files, pattern = '*.gpr$')] library (limma) #1 library (marray) #2 data= read.maim ...
microarray written 19 months ago by english.server20 • updated 19 months ago by Gordon Smyth39k

Latest awards to english.server

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: 316 users visited in the last hour