User: David

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David860
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Posts by David

<prev • 106 results • page 1 of 11 • next >
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deseq2 normalization with metagenomics data
... Hi, I´m running a 16S experiment but have some strange results when doing quality control. Note that data load into DESeq has been filtered (adapter trimming , fastqc, removal of contaminants and phiX, chimeras..). I have observed wrong spearman correlations between tehcnical replicates so my assum ...
deseq2 written 11 weeks ago by David860 • updated 10 weeks ago by Levi Waldron460
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Phylogenetic tree from marker genes
... Hi, Trying to give a short resume of what i did: 1 - From a metgenomics illumina 2x150 bp I have cleaned reads and assembled reads into contigs. For each contig i have done gene prediction and extracted bacterial marker genes (based on Campbell et All paper). 2- With bacterial markers genes i hav ...
metagenomics phyloseq ape dist written 14 months ago by David860
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Sort each column from bar chart (stack) from lower to higher
...  I would like to sort each histogram from a stacked barplot so that each column has the higher value at the bottom. Here is an example of what i obtain that you can reproduce library(plotly) m <- matrix(0, ncol = 3, nrow = 20) m <- data.frame(m) colnames(m)= c("variable","sample","value") m$ ...
R plotly written 20 months ago by David860 • updated 19 months ago by James W. MacDonald46k
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Understand fold changes
... Hello, I have an experiments where i have 6 groups. I have followed the documentation in order to compare pairwise groups. I have normalized the data as follows ... p = cumNormStat(css) css = cumNorm(css, p = p) pd <- pData(css) mod = model.matrix(~treatment,data=pd) colnames(mod) = levels(p ...
metagenomeseq written 20 months ago by David860 • updated 20 months ago by Joseph Nathaniel Paulson270
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Answer: A: FastqStreamer and qualitytype
... Ok great, Thanks so much. david   ...
written 21 months ago by David860
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FastqStreamer and qualitytype
... Hello, I have a very large fastq file  in old illumina format (ascii 64 illumina 1.5). I cannot use FastqStreamer with the qualityType. Is there any workaround ?  FastqStreamer(file, 1e+06, qualityType = "SFastqQuality") : unused argument (qualityType = "SFastqQuality")   ...
shortread written 21 months ago by David860
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Add title to enrichMap and cnetplot plots
... Hello, In the following plot how can i add a title to the graph. Both the title and main attributes are not accepted enrichMap(x, layout=igraph::layout.kamada.kawai, vertex.label.cex = 1) cnetplot(ego2...)   thanks,   ...
clusterprofiler written 22 months ago by David860 • updated 22 months ago by Guangchuang Yu990
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ReactomePA - Change colors in barplot
... Hi, barplot(x, showCategory=8)   how do you set a new color palette and discard the default ?? ...
reactomepa written 22 months ago by David860 • updated 22 months ago by Guangchuang Yu990
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Answer: A: Returning less assigned genes than expected
... Ok got the problem. I have duplicated geneIDS so the number of input ids is different from the returned number of entries.  geneID = c("1","2","3","3") allgenes = bitr(geneID, toType="SYMBOL", fromType="ENTREZID", OrgDb="org.Hs.eg.db",drop=FALSE) 'select()' returned 1:1 mapping between keys and ...
written 22 months ago by David860
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Returning less assigned genes than expected
... Hi, length(res$geneID) [1] 45487 allgenes = bitr(res$geneID, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Hs.eg.db",drop=FALSE) 'select()' returned 1:many mapping between keys and columns Warning message: In bitr(res$geneID, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = "org.Hs.eg ...
clusterprofiler written 22 months ago by David860

Latest awards to David

Popular Question 14 months ago, created a question with more than 1,000 views. For boxplot expressionset
Popular Question 14 months ago, created a question with more than 1,000 views. For fastq files
Popular Question 19 months ago, created a question with more than 1,000 views. For boxplot expressionset
Centurion 2.3 years ago, created 100 posts.

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