User: Mehmet Ilyas Cosacak

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Germany/Dresden/ CRTD - DZNE
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Posts by Mehmet Ilyas Cosacak

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Answer: A: monocle: Error in if (cds@expressionFamily@vfamily %in% c("negbinomial", "negbin
... The problem is: there are several changes in the functions of monocle. For instance; es.mef <- new("CellDataSet",as.matrix(expression.data), phenoData = pd,featureData = fd, expressionFamily = negbinomial()) es.mef <- newCellDataSet(as.matrix(expression.data), phenoData = pd,featureData = f ...
written 9 months ago by Mehmet Ilyas Cosacak0
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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 9 months ago by Mehmet Ilyas Cosacak0
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Comment: C: different statiscal results in DESeq2 from the same samples
... Thanks a lot for your suggestions. best, ilyas. ...
written 13 months ago by Mehmet Ilyas Cosacak0
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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 13 months ago by Mehmet Ilyas Cosacak0
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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 13 months ago by Mehmet Ilyas Cosacak0
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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 13 months ago by Mehmet Ilyas Cosacak0 • updated 13 months ago by Michael Love20k
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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 2.2 years ago by Mehmet Ilyas Cosacak0
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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 2.3 years ago by Mehmet Ilyas Cosacak0
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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 2.3 years ago by Mehmet Ilyas Cosacak0
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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 2.4 years ago by Mehmet Ilyas Cosacak0 • updated 2.3 years ago by Martin Morgan ♦♦ 22k

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