User: Bio_Ram

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Bio_Ram0
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Posts by Bio_Ram

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DE genes comparison of different treatments from microarray and RNAseq data
... Hi, I did RNAseq (single end) for a drug treatment (Drug A) on a cell line to look for the gene expression changes. From the literature, i found some Microarray data on the same cell line treated with other drugs (Drug B, C, D). I analysed the data of microarray data of this Drug B,C, D samples se ...
microarray limma edger deseq2 written 27 days ago by Bio_Ram0 • updated 27 days ago by James W. MacDonald47k
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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 13 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 13 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 14 months ago by Bio_Ram0 • updated 14 months ago by Michael Love19k
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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 15 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 15 months ago by Bio_Ram0 • updated 15 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 15 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 16 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 16 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 16 months ago by Bio_Ram0 • updated 16 months ago by Michael Love19k

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