User: ofonov

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Posts by ofonov

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Comment: C: DESeq2 time series analysis
... Hi, I have another question regarding time series analysis. I would like to find out difference across time points, without taking into accout Genotype and Family. In other words, hypothesis is that there is a difference between time points. Searching through the documentation and other questions, I ...
written 9 weeks ago by ofonov0
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Comment: C: DESeq2 time series analysis
... Hi Michael, I have a follow up question. I would like to take one more variable to the model - Family: B or C, so that my colData looks like colData[sample(nrow(colData), 10), ] # A tibble: 10 x 5 ID Family Genotype Time Replicate <fctr> <fctr> <fctr> <fctr> ...
written 10 weeks ago by ofonov0
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Comment: C: DESeq2 time series analysis
... Thank you for the rapid reply. What would be the best option to select top DEGs in case when adjusted p-values are high, or does it mean that this analysis is meaningless? E.g I am interested in following test, and get output with padj=0.9975788: > res_Genotype_RR_vs_SS<-results(dds, name=" ...
written 12 weeks ago by ofonov0
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DESeq2 time series analysis
... Hi, I would like to do a time-series analysis in DESeq2. I have following experimental design: Genotype: RR, SS Time: 0, 1, 7, 20 days There are 6 biological replicates for each time point. I would like to find a list of DEGs between genotypes taking into account time. For that I followed an exam ...
timecourse deseq2 multiple time points time written 12 weeks ago by ofonov0 • updated 12 weeks ago by Michael Love13k
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Differential expression of one group agains all samples
... Hi, I would like to do differential expression analysis of one group of samples (miRNA) against all samples in the dataset (e.g samples A,B,C, against samples A...K ). At the moment I have tried to use DESeq2 for this purpure. I did not find description of such possibility in DEseq2 manual, however ...
mirna deseq2 differential gene expression written 12 months ago by ofonov0 • updated 12 months ago by Gavin Kelly310
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Comment: C: [DESeq2] Multi-factor designs
... Hi, thanks for pointing out that there are 6 cell lines, for this analysis I have removed 3 cell lines which are known to be "partial responders" and can affect the analysis (I have corrected the original question). I would like to find genes for which the change in regulation differs between respo ...
written 17 months ago by ofonov0
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Answer: A: [DESeq2] Multi-factor designs
... Hi! Thanks for the reply, here is output of the commands: > packageVersion("DESeq2") [1] ‘1.10.1’ > as.data.frame(colData(dds))    names cell.line treatment responders 1    1_1 Colo320DM   CONTROL       RESP 2    1_2 Colo320DM   CONTROL       RESP 3    1_3 Colo320DM   TREATED       RESP 4    ...
written 17 months ago by ofonov0
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[DESeq2] Multi-factor designs
... I have RNA-seq dataset with 3 factors: Treatment: control , treatment (2 levels) Cell lines: ABC.1, Colo320DM, HCT.8, OU31, OVCAR4, RKO (6 levels) Groups: I, II (2 levels, so that cell lines ABC.1, Colo320DM, OVCAR4, OU31 belong to group I and RKO, HCT.8 to group II). I would like to find out ...
deseq2 multifactorial design written 17 months ago by ofonov0

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