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Search: Posts Made By: lgoff
Forum: Bioinformatics 01-25-2016, 12:25 PM
Replies: 8
Views: 2,776
Posted By lgoff
Really interesting project. Looking forward to...

Really interesting project. Looking forward to contributing to it's development. Thanks for picking up this mantle.

-Loyal
Forum: Bioinformatics 11-05-2014, 09:18 AM
Replies: 46
Views: 15,458
Posted By lgoff
Hi All, Quick update. The patched version of...

Hi All,
Quick update. The patched version of cummeRbund (release 2.8.2) is now up at bioconductor and passes all builds and checks:
...
Forum: Bioinformatics 11-03-2014, 01:33 PM
Replies: 9
Views: 7,919
Posted By lgoff
Hi all, I think i've patched cummeRbund for...

Hi all,
I think i've patched cummeRbund for RSQLite 1.0.0 compatibility. It now builds and runs on my machine. I pushed it up to BioC, but it may take a few days to get through the nightly build...
Forum: Bioinformatics 11-03-2014, 01:31 PM
Replies: 46
Views: 15,458
Posted By lgoff
Hi all, I think i've patched cummeRbund for...

Hi all,
I think i've patched cummeRbund for RSQLite 1.0.0 compatibility. It now builds and runs on my machine. I pushed it up to BioC, but it may take a few days to get through the nightly build...
Forum: Bioinformatics 10-30-2014, 11:32 AM
Replies: 46
Views: 15,458
Posted By lgoff
Great work around! Thanks for the tip. ...

Great work around! Thanks for the tip.

-Loyal
Forum: Bioinformatics 10-30-2014, 11:06 AM
Replies: 46
Views: 15,458
Posted By lgoff
Ooo! Also a good time to point out that the...

Ooo! Also a good time to point out that the cummeRbund code is now on github (http://www.github.com/gofflab/cummeRbund), should anyone be interested in taking a peek or patching it themselves. I'm...
Forum: Bioinformatics 10-30-2014, 11:03 AM
Replies: 46
Views: 15,458
Posted By lgoff
Confirmed...and yes..the cummeRbund developers...

Confirmed...and yes..the cummeRbund developers (me and ONLY me) are working on it. It's not just the sqliteQuickSQL method however, there were a number of major changes in RSQLite that have...
Forum: Bioinformatics 10-30-2014, 10:54 AM
Replies: 46
Views: 15,458
Posted By lgoff
Thanks again BrianU...

Thanks again BrianU...
Forum: Bioinformatics 10-30-2014, 10:52 AM
Replies: 46
Views: 15,458
Posted By lgoff
Fix is in the works...

Hi Guys,
Apologies for not catching this sooner, but it's been brought to my attention that there was a major overhaul of RSQLite with the release of version 1.0.0. This broke a good deal of...
Forum: Bioinformatics 05-14-2014, 01:39 PM
Replies: 32
Views: 32,297
Posted By lgoff
Hi AddDNAse, Can you provide a bit more context...

Hi AddDNAse, Can you provide a bit more context here. How are you generating this list of tracking_id and gene_short_names. Can you find a gene by gene_short_name using findGene()? Can you post a...
Forum: Bioinformatics 05-30-2013, 06:03 PM
Replies: 1
Views: 1,607
Posted By lgoff
Can you post the first few lines of your...

Can you post the first few lines of your gene_exp.diff file? It may be something in there. I'll be happy to take a look...


Loyal
Forum: RNA Sequencing 04-10-2013, 06:41 PM
Replies: 1
Views: 1,187
Posted By lgoff
Check out the 'sampleIdList' argument to...

Check out the 'sampleIdList' argument to getGenes(). This should do what you require.

Cheers,
Loyal
Forum: Bioinformatics 02-06-2013, 06:16 PM
Replies: 6
Views: 3,336
Posted By lgoff
Try another call to readCufflinks() ...

Try another call to readCufflinks()

cuff<-readCufflinks()

This will reset the DB connection and you should be good to go.

This problem arises when a previous query has produced an error. I...
Forum: RNA Sequencing 01-17-2013, 07:06 AM
Replies: 61
Views: 32,936
Posted By lgoff
Can you post the lines of the .gtf file that...

Can you post the lines of the .gtf file that correspond to the gene_id 'XLOC_000020'

grep "XLOC_000020" ./Homo_sapiens.GRCh37.68.clean.gtf

I'd like to see what the structure of your .gtf file...
Forum: RNA Sequencing 01-17-2013, 06:01 AM
Replies: 61
Views: 32,936
Posted By lgoff
Hi guys, Please make sure that when you are...

Hi guys,
Please make sure that when you are building your cuffData.db file (with readCufflinks()) that you are providing values to both the 'gtfFile' and 'genome' arguments. Also, the .gtf file...
Forum: Bioinformatics 12-11-2012, 04:48 AM
Replies: 1
Views: 1,515
Posted By lgoff
You can use the -L argument to cuffdiff to add...

You can use the -L argument to cuffdiff to add labels to your conditions...
Forum: Bioinformatics 10-11-2012, 06:50 AM
Replies: 5
Views: 17,275
Posted By lgoff
This is a similar situation in the volcano plot,...

This is a similar situation in the volcano plot, with the exception that this warning is not arising from zero-values, but rather we restrict the axes to make the plot a bit more visually...
Forum: Bioinformatics 10-08-2012, 09:35 AM
Replies: 14
Views: 9,004
Posted By lgoff
This is the file that you want to pass to...

This is the file that you want to pass to readCufflinks() since this is the one that cuffdiff used to quantify....that way, the identifiers are consistent...

-Loyal
Forum: RNA Sequencing 10-08-2012, 09:24 AM
Replies: 61
Views: 32,936
Posted By lgoff
tankman, Can you send me your cuffData.db file?...

tankman,
Can you send me your cuffData.db file? I will try to see if I can pinpoint the problem.

Thanks

-Loyal
Forum: Bioinformatics 10-08-2012, 08:38 AM
Replies: 14
Views: 9,004
Posted By lgoff
It looks like the .gtf file that you passed to...

It looks like the .gtf file that you passed to readCufflinks() might not have been the same one that was used for your cuffdiff analysis... is this the case?

The cuffdiff looks like it was using...
Forum: Bioinformatics 10-07-2012, 05:20 PM
Replies: 14
Views: 9,004
Posted By lgoff
Hi clsppb, It's entirely possible that this is...

Hi clsppb,
It's entirely possible that this is an issue with the genome name, but I'd have to look at your cuffData.db file to get a bit more information. Can you possibly send it my way?

Also,...
Forum: Bioinformatics 09-27-2012, 04:51 PM
Replies: 6
Views: 3,328
Posted By lgoff
Hi all, both PCA and MDS are now built in to the...

Hi all, both PCA and MDS are now built in to the development version of cummerbund. (PCAplot and MDSplot). Will become release version on October 2nd, but can be downloaded from BioC now...

-Loyal
Forum: RNA Sequencing 08-08-2012, 04:43 PM
Replies: 61
Views: 32,936
Posted By lgoff
I'm curious as to where the ")" is coming from. ...

I'm curious as to where the ")" is coming from. Is this somewhere in your 'myGenes'?

-Loyal
Forum: RNA Sequencing 08-08-2012, 04:41 PM
Replies: 5
Views: 4,007
Posted By lgoff
Hi Nick, I have seen this error only once...

Hi Nick,
I have seen this error only once before and the issue in this case was that the database was on an NFS mount that was interfering with the normal operation of the SQLite database. Is your...
Forum: Bioinformatics 08-08-2012, 04:38 PM
Replies: 2
Views: 1,301
Posted By lgoff
Can you confirm that you have write permissions...

Can you confirm that you have write permissions to this directory?

-Loyal
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