SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 15 of 15
Search took 0.00 seconds.
Search: Posts Made By: Mudita
Forum: Introductions 04-23-2014, 10:49 PM
Replies: 18
Views: 4,411
Posted By Mudita
Dear Alejandro, I would like to know about...

Dear Alejandro,

I would like to know about terminology used while plotting like 'fitted expression', fitted splicing' etc. I could not find the details in DEXSeq vignette.
Could you please point...
Forum: Introductions 04-14-2014, 10:42 PM
Replies: 18
Views: 4,411
Posted By Mudita
Dear Alejandro, generating the plot with pdf...

Dear Alejandro,

generating the plot with pdf format, works correctly

Thank you again,
Mudita
Forum: Introductions 04-14-2014, 01:15 AM
Replies: 18
Views: 4,411
Posted By Mudita
Thank you, Please find below the response: ...

Thank you,
Please find below the response:

code to plot:
plotDEXSeq(test, "ENSG00000167613")

warning while generating the plot:

Warning message:
In segments(intervals[rango], matr[rango,...
Forum: Introductions 04-14-2014, 12:12 AM
Replies: 18
Views: 4,411
Posted By Mudita
hello again, I am trying to generate plot in...

hello again,

I am trying to generate plot in DEXSeq, but I do not see the distribution of expression.
could you please let me know why?

2983

Thank you,
Regards,
Mudita
Forum: Introductions 04-06-2014, 10:33 PM
Replies: 18
Views: 4,411
Posted By Mudita
yes, everything works now. Thanks a lot for all...

yes, everything works now.
Thanks a lot for all your help.
Forum: Introductions 03-27-2014, 10:11 PM
Replies: 18
Views: 4,411
Posted By Mudita
Dear Areyes, I have tried as suggested....

Dear Areyes,

I have tried as suggested. However, I am getting all NA values for p and p adjusted columns.
I am using the R script below.

#!/usr/bin/env Rscript
library(DEXSeq)
...
Forum: Introductions 03-25-2014, 04:01 AM
Replies: 18
Views: 4,411
Posted By Mudita
Thank you Devon, I understand that I should...

Thank you Devon,

I understand that I should apply this formula while calculating dispersion as well as testing for differential expression:
formula=count ~ sample+group*exon+condition

Regards,...
Forum: Introductions 03-24-2014, 03:02 AM
Replies: 18
Views: 4,411
Posted By Mudita
I am sorry for late reply. Please find the...

I am sorry for late reply.
Please find the response below.

Output of sessionInfo::

Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_IN LC_NUMERIC=C ...
Forum: Introductions 03-14-2014, 05:17 AM
Replies: 18
Views: 4,411
Posted By Mudita
Dear Areyes, I would like to run paired sample...

Dear Areyes,
I would like to run paired sample analysis in DEXSeq.
I could find from this thred (http://seqanswers.com/forums/showthread.php?t=13299) that following link should be useful....
Forum: Introductions 03-10-2014, 04:05 AM
Replies: 18
Views: 4,411
Posted By Mudita
Thank you so much for your reply. However, I...

Thank you so much for your reply.
However, I just found the difference from non aggregate genes (-r no) to aggregate genes (-r yes).

output with with -r yes:...
Forum: Introductions 03-10-2014, 12:21 AM
Replies: 18
Views: 4,411
Posted By Mudita
Usage of gene aggregation option in DEXSeq

Hello Everyone,

I am using DEXSeq to find out differential usage of exons.
I want to know about the usage of gene aggregation option. After reading DEXSeq tutorial, I could understand that if I...
Forum: Introductions 04-18-2013, 04:37 AM
Replies: 4
Views: 1,564
Posted By Mudita
Thank you very much it is working now. But...

Thank you very much

it is working now. But it was just the matter of hyphen (-) before output file. I would have never figure it out.
Thanks again.

I would like to ask one more question here....
Forum: Introductions 04-18-2013, 03:34 AM
Replies: 4
Views: 1,564
Posted By Mudita
Thanks for your reply However, my bam file...

Thanks for your reply

However, my bam file is already sorted by read name. Same kind of input i have already given to htseq and it worked there. The only difference of input I could see from HTSeq...
Forum: Introductions 04-18-2013, 01:55 AM
Replies: 4
Views: 1,564
Posted By Mudita
Error while running DEXSeq

I am working with Illumina RNAseq data. My experiment contain 5-5 biological replicates of normal and treated. Initially I followed cufflink-->cuffdiff workflow...
Forum: RNA Sequencing 03-07-2013, 09:08 PM
Replies: 4
Views: 3,484
Posted By Mudita
answer for the same

Dear Sir,

Have you managed to get answer for this. We are looking for answer of similar question.

Thank you,
Mudita
Showing results 1 to 15 of 15

 


All times are GMT -8. The time now is 11:00 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO