User: Bioinfo

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Bioinfo240
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Posts by Bioinfo

<prev • 228 results • page 1 of 23 • next >
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Comment: C: Expression of a gene across all cancer datasets
... Hi genomax, I'm not able to find that Data option to download the expression data now. [http://www.cbioportal.org/index.do?session_id=5b9f65a0498eb8b3d567e16f&show_samples=false&clinicallist=CANCER_STUDY%2CPROFILED_IN_MUTATION_EXTENDED] Could you please have a look what could be the reaso ...
written 5 days ago by Bioinfo240
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Comment: C: FPKM matrix after stringtie using ballgown
... Thankyou, will follow that. ...
written 25 days ago by Bioinfo240
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Comment: C: FPKM matrix after stringtie using ballgown
... Or can I use `t_data.ctab` which has transcripts and FPKM also. I can cut the two columns for each sample and then join all into a single file? Like mentioned here [FPKM matrix][1] (Check the last comment) [1]: https://www.biostars.org/p/326375/ ...
written 25 days ago by Bioinfo240
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Comment: C: FPKM matrix after stringtie using ballgown
... Yes I understand that. I have almost 1200 samples. I didn't use -A argument with stringtie. I have the ballgown outputs. Should I run stringtie again with -A? ...
written 25 days ago by Bioinfo240
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Comment: C: FPKM matrix after stringtie using ballgown
... But with stringtie I didn't pass that argument. I have the above mentioned files and trying to use ballgown to get FPKM matrix. It is mentioned in this [FPKM matrix][1] [1]: https://www.biostars.org/p/326375/ ...
written 25 days ago by Bioinfo240
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FPKM matrix after stringtie using ballgown
... Hi, After `stringtie` step, I estimated transcript abundances and created table counts for `Ballgown`. In a folder "ballgown", I have the all the sample subdirectories inside this folder "ballgown". Each sample subdirectory have following files: e2t.ctab e_data.ctab i2t.ctab ...
stringtie ballgown fpkm rna-seq written 25 days ago by Bioinfo240 • updated 25 days ago by Adrian Pelin2.2k
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Expression of a gene across all cancer datasets
... I want to make a boxplot to show the expression of a gene across different TCGA cancer datasets. Is there any R package for that or Is there any easier way for that? There is an R package `RTCGA` for that. But only few cancer datasets are available with that. Do I need to download all the cancer da ...
R tcga geneexpression rna-seq cancer written 7 weeks ago by Bioinfo240 • updated 7 weeks ago by mmfansler220
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Comment: C: Samples with same TCGA barcode in TCGA data
... Check this [if multiple aliquots exist ][1] [1]: https://confluence.broadinstitute.org/display/GDAC/FAQ#FAQ-sampleTypesQWhatTCGAsampletypesareFirehosepipelinesexecutedupon ...
written 9 weeks ago by Bioinfo240
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Comment: C: Expression of specific genes between tumor and normal
... Sure. how to normalize count data in edgeR? And for boxplot can I plot using logCPM? ...
written 10 weeks ago by Bioinfo240
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Comment: C: Expression of specific genes between tumor and normal
... Hi Nicolas, One general question. If some wet lab scientists asked for the expression of specific genes in tumor and normal samples should I give them counts data of those genes or RPKM, FPKM, CPM, logCPM? ...
written 10 weeks ago by Bioinfo240

Latest awards to Bioinfo

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 3 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 4 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
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Popular Question 5 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: Sample names for TCGA data from GDC-legacy archive
Scholar 5 months ago, created an answer that has been accepted. For C: Sample names for TCGA data from GDC-legacy archive
Popular Question 7 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 7 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
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