User: Tom_L

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Tom_L190
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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 9 weeks ago by Tom_L190
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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 9 weeks ago by Tom_L190
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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 11 weeks ago by Tom_L190
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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 12 weeks ago by Tom_L190
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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 12 weeks ago by Tom_L190
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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 12 weeks ago by Tom_L190
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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 4 months ago by Tom_L190
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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 4 months ago by Tom_L190
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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 4 months ago by Tom_L190
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Comment: C: Strand specific pair end Illumina sequencing
... R1 is left, R2 is right. ...
written 4 months ago by Tom_L190

Latest awards to Tom_L

Appreciated 9 weeks ago, created a post with more than 5 votes. For A: How can I integrate gene with PPI network
Scholar 12 weeks ago, created an answer that has been accepted. For A: Getting sample information from GEO
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: How can I integrate gene with PPI network
Teacher 9 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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