User: Tom_L

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Tom_L180
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Posts by Tom_L

<prev • 26 results • page 1 of 3 • next >
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Answer: A: Bam to fastq conversion is giving error?
... No big deal, you just have to sort your bam by read names before converting data as recommended by bedtools (http://bedtools.readthedocs.io/en/latest/content/tools/bamtofastq.html). > BAM should be sorted by query name (samtools sort -n aln.bam aln.qsort) if creating paired FASTQ with this opti ...
written 15 days ago by Tom_L180
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Answer: A: determining cutoff for Kaplan Meier
... Considering gene expression, you should primarily rely on unsupervised approaches such as mean or median split (commonly used). However, I would not recommend the median split since you arbitrary split your cohort in half and I guess that not exactly 50% of patients will survive in your analysis. I ...
written 15 days ago by Tom_L180
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GSEA signal strength
... Hello, I have trouble understanding one of the most important GSEA metrics: the signal strength. According to the documentation (http://software.broadinstitute.org/gsea/doc/GSEAUserGuideTEXT.htm#_HTML_Report): > The enrichment signal strength that combines the two previous statistics: (Tag %) × ...
gsea written 25 days ago by Tom_L180
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Comment: C: Getting sample information from GEO
... No problem. GEOquery actually does the job but requires downloading the SOFT files first. It does not directly query GEO. Moreover: it downloads a 100Mb file per sample if you process them individually. 873 samples times 100Mb each is 87Gb, much more than the 36Gb file available from GEO (whole data ...
written 4 weeks ago by Tom_L180
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Answer: A: Getting sample information from GEO
... I answer my own question since I found a convenient way to do that. There are two problems with the GEOquery package from BioConductor. First: GEOquery required downloading the whole data again (unless I missed an option to only get sample information?) and the raw dataset is nearly 100 Gb. Knowing ...
written 4 weeks ago by Tom_L180
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Getting sample information from GEO
... Hello, It is possible to get sample information from GEO (Gene Expression Omnibus) such that I can create a script to manage a batch of samples? I'm currently working on a micro-array dataset (GSE59150) containing 873 samples. It is important to me, for each sample, to know gender and ethnicity (i ...
geo ncbi written 5 weeks ago by Tom_L180
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Answer: A: How to choose a reference genome when there's no genome information in database
... Do not use a genome that is not related to your experiments, Ever. How about: http://www.ensembl.org/Gadus_morhua/Info/Index (click on "*Download DNA sequence*")? ...
written 12 weeks ago by Tom_L180
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Comment: C: Merging of datasets from same tissue/region
... I don't understand what kind of structure do want to process and obtain. I mean, it seems like your DF is already merged so why sub-setting DF1 with the first 42 columns and DF2 with other columns but a single line? ...
written 12 weeks ago by Tom_L180
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Comment: C: Merging of datasets from same tissue/region
... To merge dataframes (DF) by row names, use *DF=merge(DF1,DF2,by="row.names")*. Also, you cannot merge multiple DF like this unless you store them into a list. Make a loop and iterate on each DF you want to merge or create a list of DF and use join_all function from plyr package (https://www.rdocumen ...
written 12 weeks ago by Tom_L180
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Comment: C: Strand specific pair end Illumina sequencing
... R1 is left, R2 is right. ...
written 12 weeks ago by Tom_L180

Latest awards to Tom_L

Scholar 4 weeks ago, created an answer that has been accepted. For A: Getting sample information from GEO
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How can I integrate gene with PPI network
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How can I integrate gene with PPI network

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