User: sgujja

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sgujja20
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United States
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8 months, 2 weeks ago
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5 years, 3 months ago
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Posts by sgujja

<prev • 14 results • page 1 of 2 • next >
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Comment: C: newSCESet and SingleCellExperiment basic differences and TMM Normalization
... Hi, Can you please let me know if you have figured out the TMM normalization with the latest package. Thanks Sharvari ...
written 8 months ago by sgujja20
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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 15 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 17 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 17 months ago by sgujja20 • updated 17 months ago by genomax71k
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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 17 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 17 months ago by sgujja20 • updated 17 months ago by genomax71k
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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 17 months ago by sgujja20 • updated 15 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 2.7 years 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 2.9 years ago by sgujja20 • updated 2.9 years ago by Ron970
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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 3.2 years ago by sgujja20

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Popular Question 2.9 years ago, created a question with more than 1,000 views. For VCF to MAF conversion for ABSOLUTE

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