User: Mehmet Ilyas Cosacak

Reputation:
0
Status:
New User
Location:
Germany/Dresden/ CRTD - DZNE
Twitter:
733242043913404
Last seen:
23 hours ago
Joined:
2 years, 4 months ago
Email:
m**********@gmail.com

Posts by Mehmet Ilyas Cosacak

<prev • 32 results • page 1 of 4 • next >
0
votes
0
answers
61
views
0
answers
monocle: Error in if (cds@expressionFamily@vfamily %in% c("negbinomial", "negbinomial.size"))
... Hi, I have a problem runing monocle. The error is as below: > es.mef <- reduceDimension(es.mef,use_irlba = F) # Reduce dimensionality Error in if (cds@expressionFamily@vfamily %in% c("negbinomial", "negbinomial.size")) { :   argument is of length zero Has anyone had a problem like that or k ...
monocle written 4 days ago by Mehmet Ilyas Cosacak0
0
votes
1
answers
119
views
1
answers
Comment: C: different statiscal results in DESeq2 from the same samples
... Thanks a lot for your suggestions. best, ilyas. ...
written 4 months ago by Mehmet Ilyas Cosacak0
0
votes
1
answers
119
views
1
answers
Comment: C: different statiscal results in DESeq2 from the same samples
... Hi Micheal, thanks for your replies. I am not comparing the power of DESeq2 with t.test. What I am trying to say, with high standard deviation, still we get significantly expressed genes.  Moreover, with low read numbers the DESeq2 calculates a log2FoldChange as significant.  Please check the foll ...
written 4 months ago by Mehmet Ilyas Cosacak0
0
votes
1
answers
119
views
1
answers
Comment: C: different statiscal results in DESeq2 from the same samples
... Hi Michael, thanks for the reply. Yes, it is possible to have different results. But, the difference is definitely high. 28 genes versus 428 genes! If we focus on the current one, I still think there is some statistical error. For Instance, if you use the input_file (https://www.dropbox.com/s/op ...
written 4 months ago by Mehmet Ilyas Cosacak0
2
votes
1
answer
119
views
1
answer
different statiscal results in DESeq2 from the same samples
... Hi, On 02.01.2017, I ran an analysis with DESeq2. I ran a similar analysis recently. I used the same input data for both runs! Please see "raw reads" in the excel file (https://www.dropbox.com/s/g7fyqvn1chdnesh/deseq2_bugreport_23102017.xlsx?dl=0). Even tough the normalized reads and basemean are s ...
deseq2 written 4 months ago by Mehmet Ilyas Cosacak0 • updated 4 months ago by Michael Love16k
0
votes
1
answers
339
views
1
answers
Comment: C: library size and fold changes
... Hi Gordon, I also have a similar question. I have two RNA-Seq sequenced at different times but exactly with the same protocol, except the library sizes are different. In the first experiment, I have 4 samples with three replicates with average library sizes of 11 million reads: untreated A and B ...
written 16 months ago by Mehmet Ilyas Cosacak0
0
votes
0
answers
377
views
0
answers
refGenome: Error in `row.names<-.data.frame`(`*tmp*`, value = value) : duplicate 'row.names' are not allowed
... Hi, I am trying to get gene list using geneList function from refGenome. However, I got the following error.  best, ilyas. >library("refGenome") Loading required package: doBy Loading required package: RSQLite Loading required package: DBI > ens <- ensemblGenome() > cdir <- getw ...
refgenome genelist written 18 months ago by Mehmet Ilyas Cosacak0
0
votes
1
answers
359
views
1
answers
Comment: C: Plotting only intergenic reads on chromosomes?
... Thanks Martin for the reply and suggestion. This only helps me to extract the reads. How can I plot them on the chromosomes? Is there any package you can suggest? best regards, ilyas.   ...
written 18 months ago by Mehmet Ilyas Cosacak0
3
votes
1
answer
359
views
1
answer
Plotting only intergenic reads on chromosomes?
... Hi, I have BAM files (RNA-Seq data, 75 bp reads) from alignment to Zebrafish genome. I know how to plot all reads in the BAM file on each chromosomes, using gviz. However, I want to plot only the reads that do not map to any known Genes, (exons or introns), rRNA, tRNA, etc. Specifically I am intere ...
genomegraphs rsamtools gviz bam samtools written 18 months ago by Mehmet Ilyas Cosacak0 • updated 18 months ago by Martin Morgan ♦♦ 21k
0
votes
1
answers
310
views
1
answers
Comment: C: limma & design matrix: for 2-color dyes and 4-comparisons?
... Thanks a lot Gordon! I really appreciate your help! best, ilyas. ...
written 20 months ago by Mehmet Ilyas Cosacak0

Latest awards to Mehmet Ilyas Cosacak

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 416 users visited in the last hour