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0
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0
replies
1.3k
views
Comment:
Comment: How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_R
13 months ago
Yang Shi
▴ 10
1
vote
4
replies
1.3k
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma
edgeR
RSEM
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
Yang Shi
▴ 10
0
votes
0
replies
1.3k
views
Comment:
Comment: How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_R
13 months ago
Yang Shi
▴ 10
0
votes
0
replies
632
views
Comment:
Comment: Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_R
13 months ago
Yang Shi
▴ 10
1
vote
2
replies
632
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2
limma
edgeR
RSEM
13 months ago
Yang Shi
▴ 10
0
votes
1
reply
2.2k
views
Comment:
Comment: Which is the best type of data for correlation or survival analysis
20 months ago
Yang Shi
▴ 10
0
votes
1
reply
2.2k
views
Comment:
Comment: Which is the best type of data for correlation or survival analysis
20 months ago
Yang Shi
▴ 10
4
votes
5
replies
2.2k
views
Which is the best type of data for correlation or survival analysis
TPM
RNASeq
RSEM
DESeq2
updated 20 months ago by
Michael Love
41k • written 20 months ago by
Yang Shi
▴ 10
0
votes
0
replies
1.8k
views
Comment:
Comment: GSVA perfomed on RSEM Expected Count data
21 months ago
Yang Shi
▴ 10
0
votes
1
reply
1.8k
views
Comment:
Comment: GSVA perfomed on RSEM Expected Count data
21 months ago
Yang Shi
▴ 10
0
votes
0
replies
1.8k
views
Comment:
Comment: GSVA perfomed on RSEM Expected Count data
21 months ago
Yang Shi
▴ 10
0
votes
1
reply
1.8k
views
Comment:
Comment: GSVA perfomed on RSEM Expected Count data
21 months ago
Yang Shi
▴ 10
0
votes
0
replies
1.8k
views
Comment:
Comment: GSVA perfomed on RSEM Expected Count data
21 months ago
Yang Shi
▴ 10
5
votes
9
replies
1.8k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
21 months ago
Yang Shi
▴ 10
0
votes
0
replies
1.2k
views
Comment:
Comment: How to judge DEG analysis of these samples could be done by using limma::voom
21 months ago
Yang Shi
▴ 10
2
votes
2
replies
1.2k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma
Clustering
voom
RNA-Seq
21 months ago
Yang Shi
▴ 10
0
votes
0
replies
1.3k
views
Comment:
Comment: pre-ranked GSEA or not?
21 months ago
Yang Shi
▴ 10
0
votes
1
reply
1.3k
views
Comment:
Comment: pre-ranked GSEA or not?
21 months ago
Yang Shi
▴ 10
2
votes
4
replies
1.3k
views
pre-ranked GSEA or not?
log2FC
DESeq2
GSEA
voom
limma
updated 21 months ago by
Gordon Smyth
50k • written 21 months ago by
Yang Shi
▴ 10
0
votes
0
replies
1.7k
views
Comment:
Comment: Removing the duplicated genes before limma::voom by using limma::avereps
21 months ago
Yang Shi
▴ 10
0
votes
1
reply
1.7k
views
Comment:
Comment: Removing the duplicated genes before limma::voom by using limma::avereps
21 months ago
Yang Shi
▴ 10
0
votes
1
reply
1.7k
views
Comment:
Comment: Removing the duplicated genes before limma::voom by using limma::avereps
21 months ago
Yang Shi
▴ 10
5
votes
6
replies
1.7k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM
avereps
voom
limma
RNASeq
21 months ago
Yang Shi
▴ 10
0
votes
0
replies
1.3k
views
Comment:
Comment: Doing normalization when using voom for DEG analysis?
21 months ago
Yang Shi
▴ 10
0
votes
1
reply
1.3k
views
Comment:
Comment: Doing normalization when using voom for DEG analysis?
21 months ago
Yang Shi
▴ 10
2
votes
4
replies
1.3k
views
Doing normalization when using voom for DEG analysis?
limma
RSEM
voom
Normalization
21 months ago
Yang Shi
▴ 10
0
votes
0
replies
968
views
Comment:
Comment: Can I use limma::avereps to remove dupicated genes before conduct DEG based on R
21 months ago
Yang Shi
▴ 10
0
votes
1
reply
968
views
Comment:
Comment: Can I use limma::avereps to remove dupicated genes before conduct DEG based on R
21 months ago
Yang Shi
▴ 10
3
votes
4
replies
968
views
Can I use limma::avereps to remove dupicated genes before conduct DEG based on RSEM Expected_count data?
limma
RNASeq
Expected_count
DESeq2
21 months ago
Yang Shi
▴ 10
0
votes
0
replies
2.1k
views
Comment:
Comment: Why Negative value from GSVA
21 months ago
Yang Shi
▴ 10
0
votes
1
reply
2.1k
views
Comment:
Comment: Why Negative value from GSVA
21 months ago
Yang Shi
▴ 10
3
votes
4
replies
2.1k
views
Why Negative value from GSVA
GSVA
RNASeq
edgeR
21 months ago
Yang Shi
▴ 10
0
votes
0
replies
860
views
Comment:
Comment: How to compute P/A calls at gene-level probeset of Human Gene 1.0 ST Array
22 months ago
Yang Shi
▴ 10
2
votes
2
replies
859
views
How to compute P/A calls at gene-level probeset of Human Gene 1.0 ST Array
pd.hugene.1.0.st.v1
oligo
AffymetrixChip
22 months ago
Yang Shi
▴ 10
1
vote
0
replies
1.1k
views
Comment:
Comment: Equivalence between PSDABG and Logarithmic Intensity Error (PLIER) Estimation
22 months ago
Yang Shi
▴ 10
0
votes
0
replies
1.1k
views
Comment:
Comment: Equivalence between PSDABG and Logarithmic Intensity Error (PLIER) Estimation
22 months ago
Yang Shi
▴ 10
0
votes
1
reply
1.1k
views
Comment:
Comment: Equivalence between PSDABG and Logarithmic Intensity Error (PLIER) Estimation
22 months ago
Yang Shi
▴ 10
2
votes
5
replies
1.1k
views
Equivalence between PSDABG and Logarithmic Intensity Error (PLIER) Estimation
pd.hugene.1.0.st.v1
oligo
AffymetrixChip
23 months ago • updated 22 months ago
Yang Shi
▴ 10
0
votes
0
replies
1.1k
views
Comment:
Comment: Robust Multi-array Average could get negative value or not?
23 months ago
Yang Shi
▴ 10
0
votes
1
reply
1.1k
views
Comment:
Comment: Robust Multi-array Average could get negative value or not?
23 months ago
Yang Shi
▴ 10
2
votes
4
replies
1.1k
views
Robust Multi-array Average could get negative value or not?
pd.hg.u219
oligo
AffymetrixChip
23 months ago
Yang Shi
▴ 10
0
votes
0
replies
1.9k
views
Comment:
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
23 months ago
Yang Shi
▴ 10
0
votes
1
reply
1.9k
views
Comment:
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
23 months ago
Yang Shi
▴ 10
0
votes
0
replies
1.9k
views
Comment:
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
23 months ago
Yang Shi
▴ 10
4
votes
10
replies
1.9k
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219
Microarray
oligo
AffymetrixChip
23 months ago
Yang Shi
▴ 10
0
votes
1
reply
1.9k
views
Comment:
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
23 months ago
Yang Shi
▴ 10
0
votes
1
reply
1.9k
views
Comment:
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
23 months ago
Yang Shi
▴ 10
0
votes
0
replies
1.6k
views
Comment:
Comment: Quantile Normalization after rma or not?
23 months ago
Yang Shi
▴ 10
0
votes
1
reply
1.6k
views
Comment:
Comment: Quantile Normalization after rma or not?
23 months ago
Yang Shi
▴ 10
3
votes
4
replies
1.6k
views
Quantile Normalization after rma or not?
limma
Microarray
oligo
23 months ago
Yang Shi
▴ 10
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