User: anaQ

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anaQ0
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Posts by anaQ

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Up and down regulated genes in deseq2
... This is the command line I used in order to obtain the up and down regulated genes, after extracting the differentially expressed genes: up <- subset(resultsDEG, log2FoldChange > 0) down <- subset(resultsDEG, log2FoldChange < 0) I'd like to know if i'm doing this right because somewh ...
deseq2 up-regulated down-regulate written 5 weeks ago by anaQ0 • updated 5 weeks ago by Michael Love24k
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Comment: C: Get normalized COUNTS Deseq2
... thank you so much! ...
written 6 months ago by anaQ0
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Get normalized COUNTS Deseq2
... Hi, i'm trying to get the normalized counts only, for all the replicates and genes of my data (named "14vs48)".  I'm trying this command: table_counts <- counts(results14vs48, normalized=TRUE) but i get this error message: unable to find an inherited method for function ‘counts’ for signature ...
deseq2 normalized counts written 6 months ago by anaQ0 • updated 6 months ago by Steve Lianoglou12k
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Comment: C: Dealing with genes that have Padj=NA
... can you explain with more detail what should i do? ...
written 7 months ago by anaQ0
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Comment: C: DESeq2 replicates management
... Dear Michael, i hace another question... in the results table, the column "baseMean" refers to the normalized data obtained from the input matrix? Or how can i get this values just with the normalization? ...
written 8 months ago by anaQ0
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Comment: C: DESeq2 replicates management
... thank you so much! ...
written 9 months ago by anaQ0
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Comment: C: DESeq2 replicates management
... Hi, i've been trying all the ways but i'm not sure if my command line is ok. Could you take a look? Thanks in advance I'd like to compare all stages (9d, 0d, 1d, 2d, 21d) versus "Control", separatelly.   #Load matrix > countsTable <- read.csv("htseqcount.csv", header=T, sep=",", row.name ...
written 9 months ago by anaQ0
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DESeq2 replicates management
... I'm looking for the differential gene expression in a somatic embryogenesis process. The thing is that i need to compare 5 conditions (stages) versus "control", each condition with two replicates. My question is... can i compare all in one run or do i need to compare by pares? And... how can i manag ...
deseq2 R bioconductor written 9 months ago by anaQ0 • updated 9 months ago by Michael Love24k
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Comment: C: DESeq2, problems using list argument to extract results from DESeq
... Hi, i'm having some trouble and seems to be similar to yours. Can you help me? ...
written 9 months ago by anaQ0

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