User: Merlin

gravatar for Merlin
Merlin 10
Reputation:
10
Status:
New User
Location:
Vancouver
Last seen:
3 weeks, 2 days ago
Joined:
1 year, 3 months ago
Email:
p********@operapadrepio.it

Posts by Merlin

<prev • 37 results • page 1 of 4 • next >
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Comment: C: RNAseq and heatmap
... Thank you, now the first part is clear enough, For the heatmap,I tried this code as you say but I have this result, **pheatmap(heatmap.genes) Error in hclust(d, method = method) : must have n >= 2 objects to cluster** I think is missing the information of the samples name which in my previous ...
written 28 days ago by Merlin 10
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RNAseq and heatmap
... Hi guys, When at the end of the analysis I export the results with this code: write.csv(as.data.frame(resOrdered), file="condition_treated_results.csv") I have a file containing a list of genes with Log2FC and p-value. let say I have two conditions treated and untreated (6 and ...
deseq2 rna-seq heatmap written 28 days ago by Merlin 10 • updated 28 days ago by Michael Love24k
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Comment: C: Contrast vs relevel (DESEq2)
... Hi Michael, this could happens if there are technical errors during the sample preparation is it that? I mean there are not live organisms with no RNA/DNA , is it the code correct the way I did with three groups? condition wil be the column of the txt file where the A,C and B condition are Is it ...
written 4 weeks ago by Merlin 10
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Contrast vs relevel (DESEq2)
... Hello everyone, From the vignette of DESeq2, I can either set the factor level by doing this code dds= relevel(dds$condition, ref=“untreated”) Or I can use the contrast, res <- results(dds, contrast=c("condition","treated","untreated")) Vignette says: “using contrast will additiona ...
rnaseq deseq2 written 4 weeks ago by Merlin 10 • updated 4 weeks ago by Michael Love24k
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Comment: C: How fold change is calculated in Ballgown?
... Hi Alyssa, Can you please confirming that regardless of the name of the group in the covariate, at the denominator will be always the one who comes first alphabetically, correct? thank you ...
written 4 weeks ago by Merlin 10
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Comment: C: How fold change is calculated in Ballgown?
... Hi Alyssa, Can you please confirming that regardless of the name of the group in the covariate, at the denominator will be always the one who comes first alphabetically, correct? thank you ...
written 4 weeks ago by Merlin 10
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DESeq2 setting significant p-value
... Hello everyone, I have a question about the p-value that comes out from DESeq2. Here is the command line that I use: res <- results(dds, alpha = 0.05) resultsNames(dds) resLFC <- lfcShrink(dds, coef=2, res=res, type="apeglm") resFile <-na.omit(resLFC) resFile <-res ...
deseq2 written 3 months ago by Merlin 10 • updated 3 months ago by Michael Love24k
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ReactomePA and genelist
... Hello everyone, I want to use ReactomePA after have performed differential expression analysis. From the bioconductor webite the first codes to run are this library(ReactomePA) data(geneList) de <- names(geneList)[abs(geneList) > 1.5] Is it not clear to me what kind of "geneLis ...
reactomepa written 3 months ago by Merlin 10 • updated 3 months ago by saicharanp180
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Comment: C: tximport and txOut
... Which one is the paper? probably if I want to do differential gene expression I can just use the default txOut= FALSE while if I want to do analysis at trascript level for the screening of different isoforms I need of txOut= TRUE thanks ...
written 3 months ago by Merlin 10
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tximport and txOut
... Hello, I'm using tximport before before running DESeq2. Tximport can summarize counts to gene-level by default or we can avoid gene-level summarization by setting txOut=TRUE using the original transcript level estimation. Can you please tell me what's the correct way for the analysis with DESeq ...
deseq2 tximport written 3 months ago by Merlin 10 • updated 3 months ago by Michael Love24k

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