User: sgujja

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sgujja20
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United States
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4 months ago
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4 years, 4 months ago
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Posts by sgujja

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Goseq Error: Only One Go Id Is In Enriched.Go List Multiple Times
... Hi, I have a similar issue with GOseq. Can you please let us know the solution you've found for getting more enriched GO terms. Thanks ...
written 4 months ago by sgujja20
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Comment: C: Help with OrderedList
... I did look at the other biostar post. All the entries are common in both the lists. However, in my example both the lists have only ~130 genes in common. Which is why I am using the mapping option. The mapping file has all the entries from lista and listb in the same order as in the respective lists ...
written 5 months ago by sgujja20
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Comment: C: Help with OrderedList
... I updated the list names and used the optional argument 'mapping' as an input. Running the function 'compareLists' seems to be working now. I just want to make sure that the mapping input is correct. > compareLists(listb, listc, mapping=lista) Simulating random scores... 0%.. ...
written 5 months ago by sgujja20 • updated 5 months ago by genomax57k
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Comment: C: Help with OrderedList
... Hello Lieven, The manual mentions about an optional parameter "mapping" when the two lists being compared are not the same. > – mapping: Maps identifiers between the two lists. This is a matrix with two columns. All items in ID.List1 must match to exactly one entry of column 1 of the mapping, e ...
written 5 months ago by sgujja20
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Comment: A: Help with OrderedList
... This is what I am trying to do: # mapping file lista <- read.table("list_1_2.txt", header=F,sep="\t") lista <- as.matrix(lista) > head(lista) V1 V2 [1,] "LOC101928626" "LOC101928626" [2,] "NADK" "ARHGEF10L" [3,] "PRDM1 ...
written 5 months ago by sgujja20 • updated 5 months ago by genomax57k
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Help with OrderedList
... Hi, I am trying to use OrderedList to compare two gene list which have about ~10% overlapping genes. However, I get an an error running: > compareLists(list2, list3) Error in compareLists(list2, list3) : 1 element(s) of first list not found in second Could you please help. Th ...
R written 5 months ago by sgujja20 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
... Thank you so much for the tutorial. I get this error when I run the step to extract clinical details: GSE2034_clindata=getGSEDataTables("GSE2034")[[2]][1:286,] 909 GSM36894 negative 109 0 ER+ 0 913 GSM36911 negative 80 1 ER+ 0 :3: parser error : xmlSAX2StartDocument ...
written 22 months ago by sgujja20
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Tools for classifying human and mouse reads for WGS data
... Hello, I am looking for suggestions on using tools for classifying human and mouse reads for PDX WGS data. Xenome for RNA-Seq works well.Any input on tools designed for DNA-Seq? Thanks ...
wgs pdx written 23 months ago by sgujja20 • updated 23 months ago by Ron820
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Answer: A: CELLULOID: tumor ploidy, cellularity, subclonal copy number events
... Hello, Could you please advise if this works on zebrafish genome to infer ploidy in tumor/normal samples from ExomeSeq Illumina PE reads. Appreciate all the help. Sharvari ...
written 2.3 years ago by sgujja20
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Comment: C: VCF to MAF conversion for ABSOLUTE
... Hello Daniel, Thanks for the reply. I did download Zv9 VEP annotation: /home/sg15w/.vep/danio_rerio/76_Zv9/Danio_rerio.Zv9.dna.toplevel.fa and for snpeff as well: java -Xmx2g -jar snpEff.jar download -dataDir $SNPEFF_DATA Zv9 On cloning Cyriacs repo perl vcf2maf.pl --input-vcf /project/umw_mi ...
written 3.4 years ago by sgujja20

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Popular Question 23 months ago, created a question with more than 1,000 views. For VCF to MAF conversion for ABSOLUTE

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