SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 10 of 10
Search took 0.00 seconds.
Search: Posts Made By: shilez
Forum: Bioinformatics 12-12-2014, 07:54 AM
Replies: 9
Views: 3,218
Posted By shilez
I have the same error, and the dxd object is...

I have the same error, and the dxd object is this:
class: DEXSeqDataSet
dim: 588047 4
exptData(0):
assays(1): counts
rownames(588047): ENSG00000000003:E001 ENSG00000000003:E002 ...
...
Forum: Bioinformatics 12-15-2011, 06:44 AM
Replies: 12
Views: 4,800
Posted By shilez
I got the same errors for some of my runs. It...

I got the same errors for some of my runs. It turned out to be running out of memory. For some reason, the last step of tophat-fusion to output the final results requires large memory. About half of...
Forum: Bioinformatics 09-19-2011, 06:08 PM
Replies: 1
Views: 6,028
Posted By shilez
Hey Quan, Please refer to the post ...

Hey Quan,

Please refer to the post
http://seqanswers.com/forums/showthread.php?t=13764
Nice to see u here :-)

Shile
Forum: Bioinformatics 09-08-2011, 10:42 AM
Replies: 4
Views: 2,620
Posted By shilez
Thank you, guys. Once I update the HTSeq, it...

Thank you, guys.
Once I update the HTSeq, it works fine.
However, I do got the error message "Same name found on two chromosomes".
Does it mean we need to remove the duplicated genes from the...
Forum: Bioinformatics 09-07-2011, 12:55 PM
Replies: 4
Views: 2,620
Posted By shilez
DEXSeq python script error message

When I try to run dexseq_prepare_annotation.py, I got a python error at line 29:
exons[f.iv] += ( f.attr['gene_id'], f.attr['transcript_id'] )
TypeError: unsupported operand type(s) for +=:...
Forum: Bioinformatics 08-31-2011, 06:49 AM
Replies: 7
Views: 9,030
Posted By shilez
Thank you severin! Now I can generate q value...

Thank you severin!
Now I can generate q value based on the cufflinks pvalue output, I think there is a bug in cufflinks when generating q values, possibly that they miss the line...
Forum: Bioinformatics 08-30-2011, 10:18 AM
Replies: 7
Views: 9,030
Posted By shilez
I got the same above 1 q value, would also want...

I got the same above 1 q value, would also want to know how q value is generated
Forum: Bioinformatics 08-29-2011, 07:03 AM
Replies: 3
Views: 3,111
Posted By shilez
Thanks a lot Simon! My sample size is...

Thanks a lot Simon!
My sample size is 10/subgroup without the normal tissue sequenced from the same individual.

My primary goal is gene expression analysis and transcript expression analysis.
I...
Forum: Bioinformatics 08-26-2011, 10:34 AM
Replies: 3
Views: 3,111
Posted By shilez
overdispersion and biological replicates

Hello,

I really appreciate the work of DESeq and EdgeR for taking the overdispersion into account for biological replicates. However assuming when analyzing tumor samples in a few cancer...
Forum: RNA Sequencing 08-25-2011, 06:10 PM
Replies: 0
Views: 1,913
Posted By shilez
overdispersion and biological replicates

Hi there,

I really appreciate the work of DESeq and EdgeR for taking the overdispersion into account for biological replicates. However assuming when analyzing tumor samples in a few cancer...
Showing results 1 to 10 of 10

 


All times are GMT -8. The time now is 09:28 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO