User: iti.gupta

gravatar for iti.gupta
iti.gupta10
Reputation:
10
Status:
New User
Location:
Last seen:
1 month ago
Joined:
2 years, 10 months ago
Email:
i********@igib.in

Posts by iti.gupta

<prev • 12 results • page 1 of 2 • next >
0
votes
0
answers
85
views
0
answers
Query regarding the cutoff values for the level 5 data of connectivity map
... Hello Everyone, For one of my analysis, I have used the connectivity map level 5 data. I am aware that these are moderated Z-scores (https://www.cell.com/action/showPdf?pii=S0092-8674%2817%2931309-0). However, my analysis requires a filtering step in which I have to filter the upregulated and downre ...
connectivitymap written 12 weeks ago by iti.gupta10
0
votes
1
answer
258
views
1
answers
Comment: C: Query regarding somatic variant calling
... Yes, correctly mentioned the non-tumor is the nearby normal tissue The disease in my case is the skin de-pigmentation disorder in which loss of melanocytes occur in a patchy fashion. In such a case i doubt that contamination point is something to consider I am still not very clear can you please ela ...
written 10 months ago by iti.gupta10
0
votes
1
answer
258
views
1
answer
Query regarding somatic variant calling
... Hello, I had a query regarding variant calling. I have three tissues from the same patient (Tumor, Non-Tumor, and Blood) I wanted to identify the somatic variants and distinguish them from the germ-line variants. How should i go about with the comparison? 1) Call the variants in all the 3 tissues se ...
somatic snp written 10 months ago by iti.gupta10
0
votes
0
answers
221
views
0
answers
Comment: C: Pair wise comparision using limma
... I am not getting any error But unfortunately, I am not getting the desired output. I want a single logFC and pvalue for all the 15 paired samples Also, I know some genes which for sure behave upregulated/downregulated as per the trend. Which is not the case here ...
written 11 months ago by iti.gupta10
0
votes
0
answers
221
views
0
answers
Comment: C: Pair wise comparision using limma
... Hey ben, I have checked the user guide. I was able to compare the simple case versus control. However, I was facing the issue with paired comparisons hence i posted here. The complete code is posted below > targets<-readTargets("Targets.txt") > head(targets) ...
written 11 months ago by iti.gupta10
0
votes
0
answers
221
views
0
answers
Comment: C: Pair wise comparision using limma
... Sorry for the confusion I have corrected the tissue encoding in the above posts. Also, I have used the topTable But the resulting matrix is somewhat unusual. colnames(tab) [1] "TargetID" "tissueL" "tissueNL" "patientVD18" "patientVD19" "patientVD20" [7] "patientVD22" " ...
written 11 months ago by iti.gupta10
0
votes
0
answers
221
views
0
answers
Comment: C: Pair wise comparision using limma
... My colnames for the design matrix looks like: colnames(design) [1] "tissueL" "tissueNL" "patientVD18" "patientVD19" "patientVD20" "patientVD22" [7] "patientVD23" "patientVD24" "patientVD32" "patientVD33" "patientVD37" "patientVD38" [13] "patientVD39" "patientVD40" "patientV ...
written 11 months ago by iti.gupta10 • updated 11 months ago by Benn8.0k
0
votes
0
answers
221
views
0
answers
Pair wise comparision using limma
... Hello all, I know there have been a lot of post about pair-wise comparison using limma but still I am struggling for the same. Please help!!! I am facing issue in defining the design matrix and the downstream steps. My experimental design looks like the following: Patient Tissue (same organ ...
microarray written 11 months ago by iti.gupta10
0
votes
2
answers
3.8k
views
2
answers
Comment: A: input for rMATS
... Is it mandatory that the read length should be same even when we are working with BAM files? (in case of rmats) ...
written 17 months ago by iti.gupta10
0
votes
0
answers
2.1k
views
0
answers
Comment: A: Paired end sequencing with different read length: better to trim everything to a
... Is it mandatory that the read length should be same even when we are working with BAM files? (in case of rmats) ...
written 17 months ago by iti.gupta10

Latest awards to iti.gupta

Great Question 5 months ago, created a question with more than 5,000 views. For GWAS summary statistics
Popular Question 2.2 years ago, created a question with more than 1,000 views. For GWAS summary statistics

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1414 users visited in the last hour