User: francesca.defilippis

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European Union
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2 years, 8 months ago
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3 years ago
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f*******************@unina.it

Posts by francesca.defilippis

<prev • 18 results • page 1 of 2 • next >
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retrieve kegg pathway abundances from gage analysis
... Hi! I used gage in order to perform a pathway enrichment analysis, using a table with KO numbers. Œs it possible to retrieve information about the abundance of the differential pathways? Because I have only KO numbers in my table (without all the kegg identification levels), so I don't know how to ...
pathways gage kegg written 2.7 years ago by francesca.defilippis40 • updated 2.7 years ago by Luo Weijun1.4k
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fastqSampler and writeFastq in shortread package
... Hello! I need to randomly subsample a fastq file. I'm trying to use the shortbread package. This are the commands I tried: xx=FastqSampler("~/Desktop/Silano2014_RawReads/1_S1_R1.fastq", 100) xx class: FastqSampler file: 1_S1_R1.fastq status: n=100 current=0 added=0 total=0 buffer=0 ordered: ...
shortread fastq write written 2.8 years ago by francesca.defilippis40 • updated 2.8 years ago by Martin Morgan ♦♦ 20k
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Comment: C: DESeq2 rlog transformation
... Hi Wolfgang! thanks for the reply. to address your question: 1 I have 24 samples (2 replicates x 12 conditions). They are Illumina single ends RNA seq of bacteria from cheese. I mapped the reads (after quality filtering and trimming) to the protein coding genes of the bacteria I'm interested. The ...
written 3.0 years ago by francesca.defilippis40
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DESeq2 rlog transformation
... Hi! I'd like to use the deseq2 rlog transformation in order to use the normalized matrix for pca and heatplots. I understood that I should use the raw counts as input, but I'd like to understand how the transformation takes into account the different library size.  In particular, I'd like to use ...
normalization deseq2 written 3.0 years ago by francesca.defilippis40 • updated 3.0 years ago by Wolfgang Huber13k
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Comment: C: gage pathways enrichment analysis
... Hi! I'm trying to apply the gage workflow to the full count matrix (raw counts, not the results from deseq).    I normalized the counts as described in the documentation and created my kegg gsets as above. Then I tried: counts.kegg.p <- gage(metag.normOV, gsets =kegg.ko.gs, ref = metag.normOV[ ...
written 3.0 years ago by francesca.defilippis40
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Comment: C: gage pathways enrichment analysis
... Thesev are the output: str(exp.fc)  Named num [1:238] -5.16 -5.09 -3.9 -3.81 -3.79 ...  - attr(*, "names")= chr [1:238] "K01866" "K01740" "K01892" "K01583" ...    head(exp.fc)    K01866    K01740    K01892    K01583    K00147    K00290  -5.155880 -5.086753 -3.897103 -3.808646 -3.787984 -3.112827  ...
written 3.0 years ago by francesca.defilippis40
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Comment: C: gage pathways enrichment analysis
... I'm sorry to bother you again, but I still have a table of NAs, except for setsize where there are some values                                         p.geomean stat.mean p.val q.val ko00970 Aminoacyl-tRNA biosynthesis            NA       NaN    NA    NA ko02010 ABC transporters                     ...
written 3.0 years ago by francesca.defilippis40
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Comment: C: gage pathways enrichment analysis
... I'm still having troubles. I created my gset > myg.sets=kegg.gsets(species = "ko") And then used it in the gage function fc.kegg.p <- gage(exp.fc, gsets = myg.sets, ref = NULL, samp = NULL) this is my exp.fc (fold changes from deseq) head(exp.fc)    K01866    K01740    K01892    K01583   ...
written 3.0 years ago by francesca.defilippis40
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Comment: C: gage pathways enrichment analysis
... My fc.kegg.p table is all NAs... Moreover, I have all pathways from human genome (i think, the IDs start with hsa). In the code above, where should I specify the organism? And what di I need to use, since I have mixed bacteria population? ...
written 3.0 years ago by francesca.defilippis40
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Answer: A: gage pathways enrichment analysis
... Hi followed the tutorial starting from DESeq output. > require(gage) > data(kegg.gs) > fc.kegg.p <- gage(exp.fc, gsets = kegg.gs, ref = NULL, samp = NULL) > sel <- fc.kegg.p$greater[, "q.val"] < 0.1 & + !is.na(fc.kegg.p$greater[, "q.val"]) > path.ids <- rownames(fc. ...
written 3.0 years ago by francesca.defilippis40

Latest awards to francesca.defilippis

Popular Question 2.7 years ago, created a question with more than 1,000 views. For DESeq2 output explanation
Popular Question 2.7 years ago, created a question with more than 1,000 views. For DESeq2 rlog transformation
Popular Question 2.7 years ago, created a question with more than 1,000 views. For DESeq2 rlog transformation
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Pathway enrichment in bacteria metagenomes
Popular Question 2.7 years ago, created a question with more than 1,000 views. For gage pathways enrichment analysis
Great Question 2.7 years ago, created a question with more than 5,000 views. For DESeq2 output explanation

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