User: annalisa.giampetruzzi

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Posts by annalisa.giampetruzzi

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Comment: C: DESeq2: making specific comparisons between samples that have two conditions and
... Hi Erin, I have read your post and since it is the same situation of my experiment, so I'm wondering if now you have  clearer idea than initial one after the Simon and Michael' s suggestion for the statistical analysis of your data with DESeq2. I will appreciate if you will share with me the seque ...
written 4.3 years ago by annalisa.giampetruzzi0
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Comment: C: setup condition table in deseq2 for experiment with multiple conditions
... Hi Michael, thanks for your help, and I'm sorry for the delay in giving you my feedback about your suggestion.  Since I want to be sure that I'm doing stat analysis in a correct way I'm just reporting you the sequence of command for DESeq2 analysis: > library (DESeq2) > count.data.set < ...
written 4.3 years ago by annalisa.giampetruzzi0
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Comment: C: setup condition table in deseq2 for experiment with multiple conditions
... Hi Michael, Thank for the code, I want to share with you a screen shoot of R after running the command line you suggested. Before the running your code I have write these: > count.data.set <- DESeqDataSetFromMatrix(countData=just.raw.counts, colData=column.data,design= ~ cultivar) convertin ...
written 4.4 years ago by annalisa.giampetruzzi0
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Answer: A: setup condition table in deseq2 for experiment with multiple conditions
... Hi all, thank for all comment on my question,  ...
written 4.4 years ago by annalisa.giampetruzzi0
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Comment: C: setup condition table in deseq2 for experiment with multiple conditions
... Hi James, you are right,  the aim of the study is to demonstrate that cultivar 1 is less susceptible than the cultivar 2, and possibly to identify which gene are responsible of this different behaviour against the pathogen. I'm not sure that the variability in gene expression in xylem and phloem a ...
written 4.4 years ago by annalisa.giampetruzzi0
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setup condition table in deseq2 for experiment with multiple conditions
... Hi all, I need to analyze my RNA seq data of my project consisting of: 1 pathogen (2 condition Healthy vs Infected) 2 plant cultivars 2 plant tissues 3 replicates for infected 2 replicates for Healthy Now I have the raw count data (after Bowtie alignment and Seqmonk quantitation) and I need to set ...
deseq2 multiple comparisons written 4.4 years ago by annalisa.giampetruzzi0

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