User: David_emir

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David_emir320
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Posts by David_emir

<prev • 143 results • page 1 of 15 • next >
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Comment: C: ADVOCATE R package
... [It is here][1], Its Github repository. [1]: https://github.com/califano-lab/ADVOCATE ...
written 20 hours ago by David_emir320
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ADVOCATE R package
... Hi All, I am using `ADVOCATE` R package to determine virtual expression from bulk gene expression. I am currently using TCGA-PAAD data. I have checked `ADVOCATE` manual, I am unable to understand the output generated. My question is how to interpret the output in this case? Can we use `ADVOCATE` tr ...
advocate R rna-seq written 1 day ago by David_emir320 • updated 1 day ago by ATpoint14k
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Answer: A: PanCanAtlas EBPlusPlus-corrected RNA-seq TCGA dataset
... TCGA Uses the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and FPKM Upper Quartile (FPKM-UQ) methods for Normalisation. Usually, they normalize for sequencing depth and gene length. FPKM takes into account that two reads can map to one fragment (and so it doesn’t count this f ...
written 13 days ago by David_emir320
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Comment: C: How to exclude some of breast cancer subtypes just by looking at gene expressio
... Hi Kevin, Sorry for the delayed reply, my Lab is in remotest part and to use the Internet I have to travel back to the city. Sorry again! I am using the following command lassoModel <- glmnet(x=data.matrix(step1[,-1]), y=step1$SubType, standardize=TRUE, alpha=2.0, family="multinomial") ...
written 28 days ago by David_emir320
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Comment: C: How to exclude some of breast cancer subtypes just by looking at gene expressio
... Hi Kevin, Thanks for your Help, It's such a great resource. I have built model LASSO for my data set, I am grateful for your tutorials. Thanks again! Secondly, when I got the best predictors I am not able to print it out it's saying (dgCMatrix) Sparse matrix error. I did use as.matrix() to print, bu ...
written 4 weeks ago by David_emir320
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Comment: C: Normal Samples From ICGC
... Hi Kevin, I am downloading the data from [ICGC-Pancreatic Cancer][1]. The Sequencing-based Gene Expression data file contains 91 samples. whereas the Clinical Specimen file says it also contains Solid normal samples which I am not able to download. For Example Specimen Ids such as "SP108126, SP1081 ...
written 6 weeks ago by David_emir320
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Normal Samples From ICGC
... Hi All, I am looking for downloading Only Normal Samples (RNA-seq) Raw counts for Pancreatic Adenocarcinoma from International Cancer Genome Consortium (ICGC), But, I am ending up downloading only Tumor samples file, can you guys let me know how to get Normal samples Raw counts from ICGC? Regards ...
icgc normal_samples written 7 weeks ago by David_emir320
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Comment: C: Downloding only RNA-Seq Raw counts data from ICGC
... Hope this will help others, code is here. mlr --tsv cut -o -f id4,id1,count2 then reshape -s id1,count2 input.tsv Or datamash --header-in --whitespace crosstab id4,id1 unique count2 < file Thanks for your help ...
written 10 weeks ago by David_emir320 • updated 10 weeks ago by ATpoint14k
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Answer: A: Downloding only RNA-Seq Raw counts data from ICGC
... Thanks a lot, Guys, I got a solution for this for cross-tabulation (or pivot table) using GNU Datamash and with Miller, using reshape! Dave ...
written 10 weeks ago by David_emir320
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Comment: C: Downloding only RNA-Seq Raw counts data from ICGC
... Thanks Vijay, I tried to cut and paste sample_id rows as a column but it gave me a really messed up results. ...
written 10 weeks ago by David_emir320

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