User: Bio_Ram

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Bio_Ram0
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Posts by Bio_Ram

<prev • 12 results • page 1 of 2 • next >
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Comment: C: ggplots gives errors
... Probably a space issue. as @Matthias Z mentioned. I tried and its working fine. Maybe suggestion of representing the strain and minute in different shape and color. geom_point(aes(color = strain, shape = minute)) Hope it helps!! ...
written 3 months ago by Bio_Ram0
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Comment: C: Help with design matrix dealing with 3 variables (DESeq2)
... Can you give more description on what region? If you consider only Muscle type and genotype this design will suite good design=~ genotype+ muscle +muscle:genotype You will have the expression across the genotypes in different muscle groups ...
written 3 months ago by Bio_Ram0
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DEseq2 time-series before and after Infection
... I am working on one of the previously published dataset and the experiment is like cell line with infected and control in a time course (T1=1hr,T2=4hr,T3=24hr) condition timepoint Mac.T1 ctrl T1 Mac.T1.1 ctrl T1 Mac.T1.2 ctrl T1 Mac.T2 ctrl ...
timecourse deseq2 multiple factor design written 4 months ago by Bio_Ram0 • updated 4 months ago by Michael Love15k
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Comment: C: DESeq2 plotCount() transform not output log2 transformed results correctly
... Can u put the details of your R script how you defined your samples and conditions?   ...
written 5 months ago by Bio_Ram0
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Save multiple plots into single pdf from Deseq2 analysis?
... I am doing Deseq2 analysis and would like to save all the plots in a single pdf file. For that i have written a function and try to use the function to save plots one after the other in a single pdf file. Here is the sample code and so far i was not succesful pdf="Results_Deseq2.pdf" if (!(is.null( ...
plot pdf dev.off written 5 months ago by Bio_Ram0 • updated 5 months ago by Wolfgang Huber13k
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Answer: A: DESeq2 plotCount() transform not output log2 transformed results correctly
... I think you did not mention the intgroup and so you have some problem. Try this way plotCounts(dds,"gene",intgroup = c("condition"),returnData = TRUE,transform = TRUE) ...
written 5 months ago by Bio_Ram0
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Answer: A: DESeq2: How to find out how well the model fits the data?
... The workflows below will give you better insights  https://www.bioconductor.org/help/workflows/rnaseqGene/ https://scilifelab.github.io/courses/rnaseq/labs/DEseq2 ...
written 6 months ago by Bio_Ram0
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Comment: C: deseq2 outliers problems
... Can you give us more details to understand the problem you are facing? ...
written 6 months ago by Bio_Ram0
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Differential expression after different normalization methods
... Is it possible to use only the differential expression module of Deseq2 or any other method for miRNA isoforms expression? I have normalized my data using RPM based normalization and looking to check the differential expression and log fold change. is there any methods so that i can test with more ...
deseq2 differential expression written 6 months ago by Bio_Ram0 • updated 6 months ago by Michael Love15k
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Comment: C: Differential expression (DESeq2) miRNAseq on patient samples
... It is really good question. From the raw counts, i could see few miRNAs which have really high count Time point 1 and drastically go down to "Zero" in the next time point and increases again in the next one. This kind of pattern were observed in most of the miRNAs. And also based on the onco gene ex ...
written 7 months ago by Bio_Ram0

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