User: Ankit

gravatar for Ankit
Ankit140
Reputation:
140
Status:
Trusted
Location:
Last seen:
4 days, 9 hours ago
Joined:
2 years, 2 months ago
Email:
r**********@gmail.com

Posts by Ankit

<prev • 117 results • page 1 of 12 • next >
0
votes
1
answer
73
views
1
answers
Comment: C: RNA-seq and histone modifictaion
... Does public datasets contain same treatment in histone modifications of chip seq data or knockout, knockin, knockdown of your histone writer rna seq data? If yes directly correlate. If not try seeing the expression of histone writers gene in your Rnaseq data. . Eg. Setdb1 or any other writer of H3K ...
written 4 weeks ago by Ankit140
0
votes
1
answer
98
views
1
answers
Comment: C: Counting RNA-seq reads mapped to mRNAs (mouse)
... Use featurecounts or htseq-count. It needs a mouse gtf file too. You can download it from gencode or ucsc. ...
written 4 weeks ago by Ankit140
0
votes
1
answer
87
views
1
answers
Comment: C: draw consensus clustering heatmap
... Try pheatmap: https://davetang.org/muse/2018/05/15/making-a-heatmap-in-r-with-the-pheatmap-package/ ...
written 4 weeks ago by Ankit140
0
votes
1
answer
159
views
1
answers
Comment: C: p value from multiple columns using R??
... It seems it gives same p.values for all the regions? Why so? Something wrong I'm doing : My script: t.result <- apply(mymatrix, 1, function(x) t.test(mymatrix[,24:35],mymatrix[,36:39], paired=FALSE)$p.value) I applied this on large matrix 24:35 are all controls , 36:39 are all cases. Is ...
written 5 weeks ago by Ankit140
0
votes
1
answer
159
views
1
answers
Comment: C: p value from multiple columns using R??
... Thanks for suggestion. My data is a methylation array. But after the subtraction from control average, the values becomes positive or negative. Now these are neither the counts, or normalized expression values or beta values or M values. They are just integers values obtained after subtractions. ...
written 5 weeks ago by Ankit140
0
votes
1
answer
159
views
1
answers
Comment: C: p value from multiple columns using R??
... OK can you share the R script for that? It will be very helpful. I tried this: myp.values <- apply(mymatrix[,1:6], 1, function(x) t.test(x[,1:3],x[,4:6], paired=FALSE)) But it does not seems to be working. ...
written 5 weeks ago by Ankit140
0
votes
1
answer
159
views
1
answers
Comment: C: p value from multiple columns using R??
... Hi Sam, Please see my above comment for comparison purposes. Basically I want to compare S1-S3 v/s S4-S6 for each row and add p.value in parallel column. Then apply benjamini hochberg for multiple correction ...
written 5 weeks ago by Ankit140
0
votes
1
answer
159
views
1
answers
Comment: C: p value from multiple columns using R??
... Compare S1,S2,S3 (control) with respect to S4,S5,S6 (cases). Basically before getting this matrix. 1. I took average of all controls (S1 - S3). 2. Subtracted all control individually from average.eg Cntrlavg -S1, Cntrlavg -S2, Cntrlavg -S3 = Control Set 3. Subtracted all cases individually from ...
written 5 weeks ago by Ankit140
0
votes
1
answer
159
views
1
answers
Comment: C: p value from multiple columns using R??
... If you have other suggestions please let me know for 6 or more samples? ...
written 5 weeks ago by Ankit140
0
votes
1
answer
159
views
1
answers
Comment: C: p value from multiple columns using R??
... I would like to apply unpaired two tailed t.test ...
written 5 weeks ago by Ankit140

Latest awards to Ankit

Centurion 7 weeks ago, created 100 posts.
Popular Question 4 months ago, created a question with more than 1,000 views. For How to extract uniquely mapped reads in Bowtie2
Popular Question 5 months ago, created a question with more than 1,000 views. For Normalisation of RNAseq data and NOIseq
Supporter 6 months ago, voted at least 25 times.
Popular Question 11 months ago, created a question with more than 1,000 views. For Normalisation of RNAseq data and NOIseq
Popular Question 16 months ago, created a question with more than 1,000 views. For Normalisation of RNAseq data and NOIseq

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 717 users visited in the last hour