User: spriyansh29
spriyansh29 • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- Last seen:
- 1 month ago
- Joined:
- 1 year, 8 months ago
- Email:
- s**********@gmail.com
Posts by spriyansh29
<prev
• 20 results •
page 1 of 2 •
next >
0
votes
0
answers
18
views
0
answers
Comment:
C: Probability in Genomics
... Not really! Just figuring out how to get started? Any leads? ...
written 5 weeks ago by
spriyansh29 • 30
0
votes
1
answer
144
views
1
answers
... ```# Merging```
```annotated <- as.data.frame(annotated %>%```
```group_by(Gene.symbol) %>%```
```filter(across(c("logFC"), ~ n_distinct(sign(.)) == 1)) %>%```
```summarise(across(c("logFC","P.Value","adj.P.Val","B","AveExpr","t"), mean), X = str_c(X, collapse= " | "),```
```Gene.ti ...
written 4 months ago by
spriyansh29 • 30
0
votes
1
answer
144
views
1
answer
... After, performing the differential analysis with ```limma```. After, mapping with the feature data, I have got the data frame as follows-
```FDR``` ```Probe_ID``` ```Gene.Symbol``` ```Gene.ID```
```0.009``` ```1555272_at``` ```RSPH10B2///RSPH10B``` ```728194///222967```
```0.007``` ```1557203_at` ...
written 5 months ago by
spriyansh29 • 30
0
votes
0
answers
224
views
0
answers
... Hi! thank you, it worked.
However, after running the testing with the following code
````cont.matrix <- makeContrasts(disease_vs_healthy = (Lesional+Non.Lesional+Peri.Lesional)-(Healthy.Volunteer),levels=design)````
````fit2 <- contrasts.fit(fit, cont.matrix)````
````fit2 <- eBayes(fit2 ...
written 5 months ago by
spriyansh29 • 30
0
votes
0
answers
224
views
0
answers
... Hi! Thanks for the quick reply, I have tried by removing the ````""```` but still got the same error
Here is the ````design````
````> design````
```` Healthy Volunteer Lesional Non Lesional Peri-Lesional````
````1 1 0 0 0````
````2 ...
written 5 months ago by
spriyansh29 • 30
1
vote
0
answers
224
views
0
answers
... **About the sample**: There are 40 samples in which 10 samples are healthy controls and 30 samples are diseased (10 of type-1 + 10 of type-2 + 10 of type-3). I wish to perform differential expression analysis between the 30 diseased and 10 controls, i.e. 30_diseased_vs_10_control. The accession id o ...
written 5 months ago by
spriyansh29 • 30
2
votes
1
answer
392
views
1
answer
... I have to perform differential gene expression analysis using ````limma````. Can I use GEO Series Matrix File(s) (expression set) in the limma workflow (differential expression analysis) without actually extracting the expression set from raw ````.CEL```` files. As I can see that ````limma```` work ...
written 6 months ago by
spriyansh29 • 30
• updated
6 months ago by
Kevin Blighe ♦ 67k
0
votes
1
answer
309
views
1
answers
... I am quite new to RNA-Seq so I followed tutorials from bioconductor's website.For DESeq2 I have used ````DESeq(dds)```` and ````DESeq(dds, test="LRT", reduced = ~ 1)````. For EdgeR I have used ````glmQLFTest(fit,coef="Group2")```` and ````glmLRT(fit,coef=""Group2"")````. The plots are [Heatmap with ...
written 6 months ago by
spriyansh29 • 30
0
votes
1
answer
366
views
1
answers
... It was a hardware constraint, as STAR requires a minimum of 30Gigs of RAM. ...
written 6 months ago by
spriyansh29 • 30
3
votes
1
answer
309
views
1
answer
... I have two groups with 12 (6 + 6) samples that were generated from bulk-RNA-Seq experiments. While performing the differential expression analysis the adjusted-p-value came out to be 1 with both DESEQ2 (Wald, LRT) and EdgeR (Quasi-likelihood, LRT). After, skimming through a few posts and papers, I f ...
written 6 months ago by
spriyansh29 • 30
• updated
5 months ago by
Biostar ♦♦ 20
Latest awards to spriyansh29
Student
12 months ago,
asked a question with at least 3 up-votes.
For Identification of Human Genes ?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1096 users visited in the last hour