User: tleona3

gravatar for tleona3
tleona310
Reputation:
10
Status:
New User
Location:
Last seen:
1 month, 1 week ago
Joined:
1 year, 7 months ago
Email:
t******@uic.edu

Posts by tleona3

<prev • 7 results • page 1 of 1 • next >
0
votes
0
answers
436
views
0
answers
EDGE microarray time series analysis fit_models() ERROR
... Hi All, I'm using the bioconductor EDGE package for R to look for differentially expressed genes in a microarray time series dataset. I have a question regarding the parameters on the de_object creation using build_study {edge}. 1) How is the ind argument incorporated into the full/null model cre ...
time series microarray written 14 months ago by tleona310
1
vote
0
answers
555
views
0
answers
Comment: C: arrayanalysis.org custom CDF version
... Thanks Kevin, I ended up just doing it using Affy once I downloaded the specific custom CDF I wanted to use from Brain Array. For those who may have issues installing and applying the custom CDF, I've posted my script below. #Set working directory setwd("~/Desktop/mc") #Install Custom ...
written 17 months ago by tleona310
2
votes
0
answers
555
views
0
answers
arrayanalysis.org custom CDF version
... Hi all, I'm using this on-line module to do the pre-processing and QC of my .CEL microarray data. My question is quite simple, but I after looking through their documentation I cannot find an answer. When mapping to a custom CDF (say hgu133plus2_Hs_ENSG), how can I know which brain array version o ...
pre-processing quality control microarray written 17 months ago by tleona310
0
votes
1
answer
863
views
1
answers
Comment: C: Microarray experimental design and analysis; repeated measures ANOVA, MaSigPro
... Thanks for the helpful response! I agree that the design is quite complex, and unfortunately the patient time points were setup this way due to limitations in the IRB protocol. It gets a bit worse in that some of the sample time points in each group are missing as they were not run on the microarr ...
written 17 months ago by tleona310
0
votes
1
answer
863
views
1
answer
Microarray experimental design and analysis; repeated measures ANOVA, MaSigPro
... Hi All, I have a large RNA microarray dataset that I am planning to analyze, but am having difficulty deciding what statistical tests to perform or R packages to used based on the experimental design. The design is as follows: There are 21 patients who have had tissue biopsies performed in two dif ...
R statistics microarray masigpro anova written 18 months ago by tleona310 • updated 17 months ago by Kevin Blighe39k
0
votes
1
answer
629
views
1
answers
Comment: C: Time point microarray data correcting for batch effects
... Hi mforde84, Thanks for your response. I'm afraid I might not have been clear in my question. I was planning to use ComBat to correct for chip to chip batch effects, but based on the sample layout across chips (see original post) and my experimental question I'm looking to answer I'm worried I won' ...
written 19 months ago by tleona310
2
votes
1
answer
629
views
1
answer
Time point microarray data correcting for batch effects
... Hi All, I'm looking at an old microarray gene expression dataset and I had a question about correcting for chip to chip batch effects. The samples were run on the Affymetrix Mouse Genome 430 2.0 Array. The experimental design is the following: 3 biological replicates of both paired mouse cutaneou ...
combat microarray batch effect written 19 months ago by tleona310 • updated 19 months ago by mforde841.2k

Latest awards to tleona3

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 2.3.0
Traffic: 904 users visited in the last hour