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 4 months ago by anaQ0 • updated 4 months ago by Michael Love25k
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Comment: C: Get normalized COUNTS Deseq2
... thank you so much! ...
written 9 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 9 months ago by anaQ0 • updated 9 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 10 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 11 months ago by anaQ0
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Comment: C: DESeq2 replicates management
... thank you so much! ...
written 12 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 12 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 12 months ago by anaQ0 • updated 12 months ago by Michael Love25k
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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 12 months ago by anaQ0

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