SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 24 of 24
Search took 0.00 seconds.
Search: Posts Made By: lmolokin
Forum: Bioinformatics 12-07-2018, 09:10 AM
Replies: 1
Views: 1,076
Posted By lmolokin
Looks like a flag from an older version of...

Looks like a flag from an older version of bbduk/bbduk2 that was used with mink to look for shorter kmers at the read ends.
Forum: Bioinformatics 04-13-2016, 11:57 AM
Replies: 0
Views: 862
Posted By lmolokin
Mugsy - passing options to nucmer

Is anyone familiar with how to run Mugsy with options passed to nucmer using the flag -nucmeropts? I tried using the syntax provided in the mugsy README with their example being -nucmeropts "-l 15"...
Forum: Bioinformatics 02-20-2015, 09:32 AM
Replies: 8
Views: 11,142
Posted By lmolokin
Makes sense. Thanks Michael, always a huge help!

Makes sense. Thanks Michael, always a huge help!
Forum: Bioinformatics 02-19-2015, 01:50 PM
Replies: 8
Views: 11,142
Posted By lmolokin
These are just raw counts. Is there a way pull...

These are just raw counts. Is there a way pull the normalized counts?

Model includes subj to account for subj-to-subj variability.

The high degree of shrinkage makes more sense to me after...
Forum: Bioinformatics 02-19-2015, 01:28 PM
Replies: 8
Views: 11,142
Posted By lmolokin
Here are the individual sample counts for this...

Here are the individual sample counts for this gene:

tx|subj|counts

control|1|1,713,852|211,362

control|2|494,568|1,805,239

control|3|5,675,537|5,881,571
Forum: Bioinformatics 02-19-2015, 12:52 PM
Replies: 8
Views: 11,142
Posted By lmolokin
high count outlier

Michael,
I have a question related to LFC shrinkage but involving a high count gene instead (the gene with the highest mean in my dataset to be exact). From what I can tell, DESeq2 has deemed this...
Forum: Bioinformatics 02-13-2015, 12:22 PM
Replies: 9
Views: 2,741
Posted By lmolokin
There appeared to be a row of NAs but how is that...

There appeared to be a row of NAs but how is that possible? When I checked countData.csv,all counts were integers. Did the NAs somehow get introduced upon import?

countData = read.csv...
Forum: Bioinformatics 02-13-2015, 11:59 AM
Replies: 9
Views: 2,741
Posted By lmolokin
same error

I am getting the same error as OP. What are you guys referring to when you say NAs?

I have 24 samples: 2 treatment groups, 6 subjects with 2 time points each.

My code is as follows:
...
Forum: Bioinformatics 11-10-2014, 07:59 AM
Replies: 35
Views: 11,404
Posted By lmolokin
Hi Michael, I wanted to clarify the purpose of...

Hi Michael,
I wanted to clarify the purpose of the reduced model in my code. Since my goal was not to compare deferentially expressed genes between a full and a reduced model, I assume that the...
Forum: Bioinformatics 10-31-2014, 01:40 PM
Replies: 35
Views: 11,404
Posted By lmolokin
Gotcha. Session info below. Really appreciate...

Gotcha. Session info below. Really appreciate your help, Michael!

Aleksey

R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United...
Forum: Bioinformatics 10-31-2014, 12:25 PM
Replies: 35
Views: 11,404
Posted By lmolokin
You're right! It appears to have worked now. ...

You're right! It appears to have worked now.

I received this message after running the LRT: 32 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with...
Forum: Bioinformatics 10-31-2014, 11:49 AM
Replies: 35
Views: 11,404
Posted By lmolokin
I'm not sure I understand where the "user...

I'm not sure I understand where the "user specified model matrix" is applied to dds.

I create the dds object with a place-holder formula here:
dds <- DESeqDataSetFromMatrix(countData =...
Forum: Bioinformatics 10-31-2014, 09:29 AM
Replies: 35
Views: 11,404
Posted By lmolokin
I see. Is there no way to specify a model...

I see.

Is there no way to specify a model matrix within the DESeqDataSetFromMatrix function in lieu of a formula?
Forum: Bioinformatics 10-31-2014, 08:37 AM
Replies: 35
Views: 11,404
Posted By lmolokin
Thanks for the help thus far, Michael. Is...

Thanks for the help thus far, Michael.

Is there a way to insert the modified model.matrix into the dds object in order to test contrasts from modelMatrix=m?

In other words, so that when I call...
Forum: Bioinformatics 10-30-2014, 02:47 PM
Replies: 35
Views: 11,404
Posted By lmolokin
Thanks! Just ran through the workflow...

Thanks!

Just ran through the workflow without a hitch.

My next question is how do I specify different contrasts since resultsNames(dds) now only gives me just [1] Intercept?
Forum: Bioinformatics 10-30-2014, 02:27 PM
Replies: 35
Views: 11,404
Posted By lmolokin
Thanks for the quick reply. I see how you...

Thanks for the quick reply.

I see how you use modelMatrix after already having created the dds object. But how can I initially create the dds object if I can't specify the model within it?
...
Forum: Bioinformatics 10-30-2014, 01:55 PM
Replies: 35
Views: 11,404
Posted By lmolokin
design not of full rank

Hi,
I'm attempting to use the same formula as above (~treatment + treatment:subject + treatment:time) to get within treatment time effects while accounting for subject differences. The problem I've...
Forum: Illumina/Solexa 04-21-2014, 12:14 PM
Replies: 18
Views: 13,420
Posted By lmolokin
Thank you for your responses. So far, what...

Thank you for your responses.

So far, what I've gathered is that the appropriate method to analyze my data is to run a PROC GLIMMIX (nb distribution) repeated measures analysis. So if I understand...
Forum: Illumina/Solexa 04-09-2014, 12:56 PM
Replies: 18
Views: 13,420
Posted By lmolokin
Mixed ANOVA

Hi guys,
I'm going to revive this thread as I haven't been able to find a straight forward answer to whether it is possible to run a Mixed ANOVA-like analyses in edgeR/DESeq2.

My RNA-seq...
Forum: Bioinformatics 12-13-2012, 07:49 AM
Replies: 14
Views: 7,685
Posted By lmolokin
Wolfgang, thank you for your reply! Here's...

Wolfgang, thank you for your reply!

Here's the output:

R version 2.15.2 (2012-10-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252 ...
Forum: Bioinformatics 11-20-2012, 01:22 PM
Replies: 14
Views: 7,685
Posted By lmolokin
DESeq, experimental design

Hi Everyone,
I'm looking for some help to make sure my data frame is set up correctly. My experiment has 30 samples from 10 subjects, 3 time points each, and I want to tell the software to look for...
Forum: Sample Prep / Library Generation 09-18-2012, 03:59 PM
Replies: 18
Views: 12,968
Posted By lmolokin
Happy to help. I prefer to use vacuum...

Happy to help.

I prefer to use vacuum centrifugation to concentrate my RNA, however, when doing so try to avoid spinning the RNA under vacuum for prolonged periods of time. I also typically never...
Forum: Sample Prep / Library Generation 09-18-2012, 08:04 AM
Replies: 18
Views: 12,968
Posted By lmolokin
In my experience on-column DNase treatment is...

In my experience on-column DNase treatment is never as efficient at removing gDNA as in-solution DNase treatment. Anytime an RNA extraction protocol has an on-column DNase treatment step, I skip it,...
Forum: Sample Prep / Library Generation 09-17-2012, 09:17 AM
Replies: 11
Views: 8,568
Posted By lmolokin
GLOBINclear

I have used the GLOBINclear kit (Ambion/Life Tech) to reduce globin mRNA (HBA1/HBB) in total RNA from human blood. In my experience, most of the time the reduction works and you see less than 5%...
Showing results 1 to 24 of 24

 


All times are GMT -8. The time now is 10:10 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO