User: a.lathifbt

gravatar for a.lathifbt
a.lathifbt20
Reputation:
20
Status:
New User
Location:
Chennai, India
Last seen:
3 weeks, 3 days ago
Joined:
11 months, 2 weeks ago
Email:
a************@gmail.com

Posts by a.lathifbt

<prev • 18 results • page 1 of 2 • next >
1
vote
1
answer
1.4k
views
1
answers
Comment: C: ORF reading in Python
... This function reads just the sequence and not fasta files directly. You need to parse the fasta file and extract only the sequence before you can run the function. Hope it helps. ...
written 8 weeks ago by a.lathifbt20
0
votes
1
answer
236
views
1
answers
Comment: C: Differential Expression Analysis using Bioconductor (RStudio) and GEO2R (GEO)
... Hello Kevin! Could you kindly please clarify my doubt on which code chunk to use for the type of analysis I am working on. I'm quite new to this and really clueless about which is the right approach for my work... Thank you ...
written 11 weeks ago by a.lathifbt20
0
votes
1
answer
236
views
1
answers
Comment: C: Differential Expression Analysis using Bioconductor (RStudio) and GEO2R (GEO)
... Thank you for the suggestion, Kevin! Will make that change in the colnames. **My ultimate goal is to identify the genes that are differentially expressed in the seven POS case compared to the three normal healthy controls, so is the code chunk (top) I used does this comparison? or should I go with ...
written 11 weeks ago by a.lathifbt20
0
votes
1
answer
236
views
1
answers
Comment: C: Differential Expression Analysis using Bioconductor (RStudio) and GEO2R (GEO)
... Thank you, Kevin! The group_pheno is a data frame (which I created manually) with two columns, the first one being the sample name and the other is the disease status (case or control). > group_pheno Sample status 1 GSM850527 normal 2 ...
written 11 weeks ago by a.lathifbt20
3
votes
1
answer
236
views
1
answer
Differential Expression Analysis using Bioconductor (RStudio) and GEO2R (GEO)
... I was doing a differential gene expression analysis on a microarray dataset with three controls and 7 case samples. I used the limma package in RStudio to do the analysis. Wrote the following code based on Bioconductor vignettes and online tutorials: library(limma) edata<-exprs(grou ...
gene R bioconductor microarray deg written 11 weeks ago by a.lathifbt20 • updated 11 weeks ago by Kevin Blighe59k
0
votes
1
answer
451
views
1
answers
Comment: C: Combining different conditions of study from different experiments (same platfor
... This is out of this topics scope, but some of the datasets I have can be subdivided into groups based on their phenotype (each group include case and controls). I am using Bioconductor packages for this analysis. I understand that during the DEG estimation (using limma) I need to have these groups a ...
written 3 months ago by a.lathifbt20
0
votes
1
answer
451
views
1
answers
Comment: C: Combining different conditions of study from different experiments (same platfor
... As in I need to do the DEG analysis separately for those 10 different datasets and just find the union of the DEGs across them? I came across a paper where they did a similar study using datasets studying different tissues, but there was no clear explanation of how they went forward and interpreted ...
written 3 months ago by a.lathifbt20
0
votes
1
answer
451
views
1
answers
Comment: C: Combining different conditions of study from different experiments (same platfor
... So my design matrix formula (for limma) needs to be something like mod<-model.matrix(~as.factor(disease_status)+batch,data) #is adding the term "batch" within the matrix design enough to account for the confounders??? provided I merged all the columns (cases and controls) into a single ...
written 3 months ago by a.lathifbt20
0
votes
1
answer
451
views
1
answers
Comment: C: Combining different conditions of study from different experiments (same platfor
... Hello Kevin, Can you please elaborate on adding how to bring in batch as a covariate into the model matrix design? My work plan involves using around 10 different microarray datasets (same platform) to identify the DEGs between case and control. Each of these datasets has its own case and control ...
written 3 months ago by a.lathifbt20
0
votes
1
answer
160
views
1
answers
Comment: C: Handling Microarray datasets from different experiments for DEG analysis
... Which R package should I use for this type of Meta-analysis? ...
written 3 months ago by a.lathifbt20

Latest awards to a.lathifbt

Popular Question 12 weeks ago, created a question with more than 1,000 views. For ORF reading in Python

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1237 users visited in the last hour